Sticky rice

ABSTRACT

Restriction Independent Cloning Events (RICE) are made by generating 5′ overhangs (sticky ends). The polynucleotides to be joined are reacted with a DNA polymerase, having 3′ to 5′ exonuclease activity and 5′ to 3′ polymerizing activity, less than all of the dNTPs, a kinase (optional) and a ligase. The complementary 5′ overhangs anneal and ligate.

RELATED APPLICATIONS

[0001] The instant application claims priority to co-pending U.S.Non-provisional patent application Ser. No. 10/190,451, filed Jul. 2,2002, entitled STICKY RICE, which claims priority to U.S. provisionalpatent application No. 60/365,058 filed Mar. 13, 2002, entitled STICKYRICE, both of which are incorporated herein by reference in theirentirety.

BACKGROUND OF THE INVENTION

[0002] The present invention relates to a method of joiningpolynucleotides by reacting polynucleotides with a DNA polymerase, a DNAligase and optionally a polynucleotide kinase. Complementary 5′ cohesive(sticky) ends are generated and subsequently anneal and are ligated allin the same reaction vessel. The method allows for the formation ofRestriction Independent Cloning Events (RICE) or Restriction IndependentCohesive Ends (RICE) by reacting sticky ended polynucleotides, i.e.,Sticky RICE.

[0003] U.S. Pat. No. 5,075,227 discloses methods for cloning cDNA andproducing mRNA from the cloned c-DNA. The c-DNA is cloned in oneorientation by using a vector containing a directional cloning site andprimer-adapter sequences complementary to portions of the directionalcloning site. U.S. Pat. No. 5,075,227 describes directional sticky endcloning where sticky end (5′ overhangs) are generated by treatment oflinear double stranded (ds) DNAs with T4 DNA polymerase and only onedNTP. Sticky ends of 12-15 nucleotides are disclosed as being preferredin U.S. Pat. No. 5,075,227. However, the vector polynucleotides andinsert polynucleotides in the U.S. Pat. No. 5,075,227 are reacted withDNA polymerase separately and cannot be co-treated and the T4 DNApolymerase activity must be inactivated before the vector and insertpolynucleotides are combined.

[0004] The present invention provides an easy and quick method forjoining multiple polynucleotides in a single tube or vessel and amechanism for directional cloning without the requirement forrestriction enzymes and minimal primer modification.

SUMMARY OF THE INVENTION

[0005] Briefly, in accordance with the present invention two or moredouble stranded polynucleotides are joined by generating complementary5′ cohesive ends on two or more polynucleotides by reacting thepolynucleotides with a DNA polymerase having 3′ to 5′ exonucleaseactivity and 5′ to 3′ polymerizing activity in the presence of less thanall of the dNTPs selected from the group consisting of dGTP, dCTP, dATPand dTTP wherein complementary 5′ overhangs (cohesive ends) areproduced. The complementary cohesive ends are allowed to anneal. Theannealed polynucleotides are then ligated in the presence of DNA ligase.If the polynucleotides do not have a 5′ phosphate group, a 5′ phosphategroup may be formed in situ by adding a polynucleotide kinase to thereaction mixture.

[0006] The present process generates the complementary sticky ends usingthe 3′ to 5′ exonuclease activity of the DNA polymerase and allows thecomplementary sticky ends to anneal. The annealed complementary stickyends are then ligated with a DNA ligase. These steps can all be doneconcurrently by incubating all of the components of the reactionstogether. Alternatively, the present process can be conducted in asequential manner by first reacting the polynucleotides with the DNApolymerase, appropriate dNTP(s) and optional kinase before the DNAligase and/or kinase is added to the reaction mixture.

[0007] Of particular interest in practicing the present inventions,vector (double stranded polynucleotides) fragments and an insert doublestranded DNA fragment polynucleotide are reacted with a T4 DNApolymerase, appropriate dNTP(s), a kinase and T4 DNA ligase.Complementary 5′ overhangs are generated, and are allowed to anneal andligate resulting in insertion of the DNA insert into the vector. Thefinished vector is then used to transform a host.

BRIEF DESCRIPTION OF THE DRAWINGS

[0008]FIG. 1 is a photograph of a gel that has been digitally invertedsuch that all dark areas are light and all light areas are dark toreveal the details of the banding displayed in the gel more clearly, andshows the results of experiments as described below in Example 1A, 1B,1C and 1D, where lane 1 in FIG. 1 is Promega 100 bp DNA molecular weightladder, lane 2 shows Example 1A reaction, lane 3 shows Example 1Breaction, lane 4 shows Example 1C reaction and lane 5 shows Example IDreaction.

[0009]FIG. 2 is a diagram that represents Experiment 2A, 2B, 2C and 2Dand shows plasmid pUC 19 and relative locations and directions of theprimers used for amplification of pUC 19 by PCR for experiments inExamples 2A-2D. In the diagram, primers are represented by the solidarrows, 5′ prime (blunt end of arrow) to-3′ prime (point of arrow).Primers Seq ID NO: 18, Seq ID NO: 22, Seq ID NO: 26, and Seq ID NO: 30hybridize to pUC 19 at the location identified by primer B in FIG. 2.Primers Seq ID NO: 19, Seq ID NO: 23, Seq ID NO: 27, and Seq ID NO: 31hybridize to pUC 19 at the location identified by primer A in FIG. 2.

[0010]FIG. 3 is a photograph of a gel that has been digitally invertedsuch that all dark areas are light and all light areas are dark toreveal the details of the banding displayed in the gel more clearly, andindicates the results of experiments as described below in Example 2showing Sticky RICE cloning of inserts into pUC using T4 DNA ligase.

[0011]FIG. 4 is a photograph of a gel that has been digitally invertedsuch that all dark areas are light and all light areas are dark toreveal the details of the banding displayed in the gel more clearly. Thegel indicates the results of experiments as described below with respectto Example 3 showing Sticky RICE cloning of inserts into pUC using E.coli ligase.

[0012]FIG. 5 is a photograph of a gel that has been digitally invertedsuch that all dark areas are light and all light areas are dark toreveal the details of the banding displayed in the gel more clearly.FIG. 5 indicates the experimental results corresponding to Example 4showing Sticky RICE cloning of GFP PCR product into SapI digested vectorDNA—pLSB 1176.

[0013]FIG. 6 is a photograph of a gel that has been digitally invertedsuch that all dark areas are light and all light areas are dark toreveal the details of the banding displayed in the gel more clearly. Theresults indicated in FIG. 6 are explained in greater detail below inExample 5.

[0014]FIG. 7 is a photograph of a gel that has been digitally invertedsuch that all dark areas are light and all light areas are dark toreveal the details of the banding displayed in the gel more clearly. Theresults indicated in FIG. 7 are explained in greater detail below inExample 6.

[0015]FIG. 8A is a photograph of a gel that has been digitally invertedsuch that all dark areas are light and all light areas are dark toreveal the details of the banding displayed in the gel more clearly.FIG. 8 indicates results of directional joining of a 225 and 725 bp PCRproduct sharing a 3 bp overlap as described below in Example 7.

[0016]FIG. 8B is a flowchart showing the basic steps described inExample 7.

[0017]FIG. 9A is a photograph of a gel that has been digitally invertedsuch that all dark areas are light and all light areas are dark toreveal the details of the banding displayed in the gel more clearly.FIG. 9A indicates the results of Example 8, described in greater detailbelow.

[0018]FIG. 9B is a flowchart showing the basic steps described inExample 8.

[0019]FIG. 10A is a flowchart showing other embodiments of the methodsfor joining DNA fragments in accordance with the present invention.

[0020]FIG. 10B is a flowchart showing yet another embodiment of themethods for joining DNA fragments in accordance with the presentinvention.

[0021]FIG. 10C is a flowchart showing still another embodiment of themethods for joining DNA fragments in accordance with the presentinvention.

[0022]FIG. 10D is a flowchart showing still yet another embodiment ofthe methods for joining DNA fragments in accordance with the presentinvention.

[0023]FIG. 11 is a flowchart showing yet another embodiment of thepresent invention.

[0024]FIG. 12 is a flowchart showing yet another embodiment of thepresent invention.

[0025]FIG. 13 is a chart showing a partial sequence listing for pLSB1176 that was assembled using the methods of the present invention, withkey portions marked for discussion below.

[0026]FIG. 14 is a flowchart showing basic steps for converting PCRproducts into expressible elements without cloning in accordance withfurther embodiments of the present invention.

[0027]FIG. 15 is a flowchart that depicts a variety of combinations ofsteps for practicing the present invention in a two step process, theflowchart corresponding to Examples 9-16 of the present invention.

[0028]FIGS. 16A, 16B and 16C are flowcharts that depict a furthervariety of combinations of steps for practicing the present invention ina three step process, the flowcharts corresponding to Examples 17-33 ofthe present invention.

[0029]FIG. 17 is a flow chart that depicts a still more combinations ofsteps for practicing the present invention, the flowchart correspondingto Examples 34-41 of the present invention.

[0030]FIG. 18 is a block diagram depicting a computer and fluid handlerfor effecting the various procedures described herein in an automatedfashion.

DETAILED DESCRIPTION OF THE INVENTION

[0031] In practicing the present invention, double strandedpolynucleotides are joined by generating 5′ overhangs (cohesive orsticky ends) of defined length and sequence by employing a DNApolymerase having 3′ to 5′ exonuclease activity. This is accomplished byreacting the DNA polymerase with a linearized polynucleotide (ds DNAmolecule) and a subset of at least one type of dNTP but not more thanthree of the four dNTPs (dATP, dTTP/dUTP, dCTP or dGTP). The dsDNAmolecule can be blunt or non-blunt ended. After the 5′ overhang cohesiveends are generated the complementary cohesive ends are allowed to annealwhereby at least one of the ds DNA molecules has a 5′ phosphate group.The 5′ phosphate group can be present on the ds DNA molecule before thereaction or can be formed in situ during the reaction by addition of apolynucleotide kinase to the reaction mixture. After annealing, thecohesive ends are ligated in the presence of a DNA ligase.

[0032] The polynucleotides or ds DNA molecules to be joined according tothe present invention can be any ds polynucleotides where it would bedesirable to join them to make a longer polynucleotide molecule. Thepolynucleotides can be prepared using conventional techniques such asknown DNA synthesis techniques, DNA polymerase chain reaction (PCR) orby restriction enzyme digestion, such as, for example, with a type IISrestriction enzyme, such as Sap I or Ear I. When a restrictionendonuclease is used to make the starting polynucleotide the resultingpolynucleotide can be blunt ended or can have either a 3′ or 5′overhang. In a preferred embodiment, the polynucleotides to be joinedcomprise a vector and an insert polynucleotide wherein the insertincludes the coding region for the expression of a desirable protein orRNA molecule. Once the vector and insert polynucleotides are joinedforming a finished vector, the finished vector is used to transform ahost cell whereby the host contains the desirable coding region and iscapable of expressing the encoded protein or RNA molecule. The joinedpolynucleotide can be either linear or circular. The present process canbe used to clone a single gene of interest or to clone a library ofpolynucleotides into a suitable vector. Another preferred embodimentincludes cloning of DNA sequences which may or may not encode forprotein or RNAs.

[0033] The 5′ overhangs, also referred to as sticky ends or cohesiveends, can be 1-15 nucleotides in length and are preferably 2-8nucleotides in length. The 5′ overhangs are comprised of any of thenucleotides but can be comprised of the same nucleotide, i.e., all t's,all g's, etc.). When the '5 overhang is comprised of mixed nucleotidesit is preferred that the 5‘overhang is comprised of a’s and t's togetheror g's and c's together. The complementary 5′ overhangs allow thepolynucleotides to be joined in a directional orientation if desired.The 5′ overhang can also be self-complementary to an otherwise identicalpolynucleotide.

[0034] The following 5′ overhangs and their complementary sequence areuseful in practicing the present invention (however, other 5′ overhangscan also be used): 5′ Overhang Complementary Sequence 5′ ttt ttt aaa aaa5′  5′ gg gg cc cc 5′ 5′ cc gg 5′ 5′ aaaat tttta 5′ 5′ ggc ccg 5′ 5′ atgtac 5′ 5′ aaa ttt 5′ 5′ taa att 5′ 5′ cgg gcc 5′ 5′ gcc cgg 5′ 5′ aattta 5′

[0035] The length of the 5′ cohesive/sticky ends formed by the DNApolymerase activity is determined by the presence of one or more stopbases that occur consecutively in the polynucleotide sequence. The stopbases, in conjunction with the appropriate dNTPs, limit the 3′ to 5′exonuclease activity of the DNA polymerase enzyme thereby limiting thelength of the 5′ single stranded ends that are formed. The overhangsequences and/or stop bases are conveniently incorporated into theprimers that are used in the PCR process when PCR is employed to makethe starting polynucleotides. The overhang and stop bases can alsooverlap between the primer and original nucleotide. Alternatively, thestop bases and 5′ overhang are already in the polynucleotide when thepolynucleotides are obtained without PCR.

[0036] The following reaction scheme illustrates the role of stop basesand dNTPs in the present invention. Fragment C and Fragment Drepresented below are to be joined according to the Sticky RICE process.The stop bases in Fragment C are “GG” and the stop bases in Fragment Dare “CC.”

[0037] The dNTPs employed in the Sticky RICE process for joining theabove DNA fragments are dGTP and dCTP. The dGTP limits the exonucleaseactivity of T4 DNA polymerase on Fragment C resulting in Fragment C′having the desired 5′ overhang. The dCTP limits the exonuclease activityof the T4 DNA polymerase on Fragment D resulting in Fragment D′ having adesired 5′ overhang. The 5‘overhangs of Fragments C’ and Fragment D′ arecomplementary.

[0038] The DNA polymerase, kinase and ligase enzymes used in the presentprocess are those enzymes that are well known to one of ordinary skillin the art. The DNA polymerase will have 5′ to 3′ polymerase activityand also 3′ to 5′ exonuclease activity. Suitable DNA polymerases includebut are not limited to T4 DNA polymerase, E. coli DNA polymerase 1, theKlenow fragment of E.-coli DNA polymerase and T7 DNA polymerase. Theligase is capable of creating a phosphodiester between the 3′ hydroxylof one nucleotide and the 5′ phosphate of another nucleotide. Suitableligases include, but are not limited to, T4 DNA ligase and E. coli DNAligase. The kinase is capable of adding a phosphate group to the 5′ endof a polynucleotide. Suitable kinases include, but are not limited to,T4 polynucleotide kinase. The kinase is an optional component of thepresent method and is employed to place a phosphate group on the 5′ endof the polynucleotides if the polynucleotides do not already contain a5′ phosphate group. The kinase conveniently adds the phosphate group insitu in the reaction mixture.

[0039] In one embodiment of the present invention the DNA polymerase,polynucleotide kinase and DNA ligase reactions are accomplishedconcurrently by incubating or reacting all of the components togetherfor a time and under conditions sufficient to allow the generation ofthe complementary 5′ overhangs (cohesive ends), annealing of thecomplementary 5′ overhangs and their resulting ligation. Alternatively,the present process can be conducted sequentially where the DNApolymerase and/or kinase reaction is allowed to proceed to substantialcompletion before the DNA ligase and/or kinase reaction. The kinasereaction, if needed to add 5′ phosphate groups to the polynucleotides,is conducted either before the DNA ligase reaction or concurrentlytherewith. Alternatively the DNA polymerase and/or kinase reaction canbe performed and then the DNA polymerase and/or kinase activities can beinactivated (by a high temperature incubation step, for example 75 C for10 minutes) which is known to inactivate the DNA polymerase and/orkinase enzymes used. Following this inactivation, ligase and/or kinaseactivities can be added to the reaction.

[0040] The present process or method is conducted employing standardreactants, procedures and equipment well known to one of ordinary skillart. Buffers when employed are also well known to the skilled artisan.The temperature at which the present reactions are conducted is notcritical. Temperatures are advantageously from about 5° C. to about 50°C. and preferably from about 12° C. to about 37° C. The temperature ofthe different reactions can vary (DNA polymerase reaction conducted at adifferent temperature than the ligation reaction, for example) or theycan be conducted at substantially the same temperature. One skilled inthe art can easily determine the optimum temperature based on theparticular reactants and reagents by conducting routine experiments atvarious temperatures.

[0041] Since enzymes are involved, the length of the reaction periodwill vary inversely with the temperature, i.e., in general the higherthe temperature the quicker the reaction.

[0042] In one embodiment of the present invention a vectorpolynucleotide and an insert polynucleotide are reacted in the presenceof a subset of dNTPs, T4 DNA polymerase, a kinase and T4 DNA ligase. Thereaction mixture is incubated for 30 minutes at 37° C. and then allowedto further incubate at room temperature overnight. An alternativeincubation period would be to allow the reactants to incubate at between16° C. and ambient temperature overnight. Alternatively, the vectorpolynucleotide and the insert polynucleotide can be reacted with thesubset of d NTPs and T4 DNA polymerase at 37° C. for 30 minutes followedby the addition of T4 DNA ligase and kinase after the reaction mixturehas cooled to room temperature. This final reaction mixture is thenallowed to incubate at room temperature for 12-16 hours or overnight. Itis readily apparent that the present process allows the simultaneoustreatment of both the vector polynucleotide and the insertpolynucleotide with the DNA polymerase and dNTPs wherein thecomplementary 5′ overhangs are produced in situ. Additionally, the DNApolymerase does not need to be inactivated before the ligase reaction isallowed to proceed, but can be if so desired.

[0043] The following reaction scheme illustrates “Sticky RICE” joiningof two ds polynucleotides where ds polynucleotide Fragment A and dspolynucleotides Fragment B are joined:

[0044] The method of the present invention is useful in constructinglinear expression elements, in gene/vector assembly, for constructinggene fusions, for ligating into plasmids or phage or for any otherprocedures where a recombinant polynucleotide is the desired product.Single gene cloning or library construction can also be accomplished.The present method is adaptable, easy to use, cost effective frommaterials, time and labor perspectives and, efficient. The method allowsdirectional cloning and is seamless, i.e., no restriction sites arerequired.

[0045] In another embodiment of the present sticky RICE reaction, it maybe desirable to purify the joined DNA reaction product from the buffersand/or enzymes used in the sticky RICE reaction. This can beaccomplished by placing a suitable tag moiety (such as a biotin group,for example) on at least one of the starting material DNAs to be used inthe sticky RICE reaction. The incorporation of biotin tags intosynthetic DNAs is well known to the skilled artisan. Oligos containingone or more biotin groups are commercially available. Such biotinylatedoligos can be used in polymerase chain reactions. After the “tagged”reaction products are formed then standard purification protocolsrelating to the “tagged” products are employed. For example, a ds DNAproduct comprising an open reading frame of interest is synthesized witha biotinylated “downstream” or reverse oligonucleotide is joined with asecond ds DNA product which contains additional vector components, forexample, a phage RNA polymerase promoter sequence (such as the T7, SP6or T3 RNA polymerase promoters) according to the present Sticky RICEprocess resulting in the ligation of the two DNA fragments. Thebiotinylated DNA product is readily purified from the sticky RICEreaction components by a variety of known reagents, such as magneticbeads coated with avidin or streptavidin molecules. After collecting themagnetic beads to which the biotinylated DNAs are now bound, the beadsare washed and ultimately transferred into a separate reaction, such asan in vitro transcription reaction, for example. Streptavidin coatedmagnetic beads and protocols for their use in purification ofbiotinylated DNAs are available from a number of commercial suppliers,including the Promega Corporation (Madison, Wis., USA), and Dynal (LakeSuccess, NY, USA).

[0046] The present invention can be employed to generate directionalcloning kits using a desired vector. These kits would facilitate the useof the vectors for whatever their intended purpose (for example libraryconstruction, cloning genes for expression of proteins in animal, plantor bacterial cells, etc.) by making the cloning process easier and moreefficient. A cloning kit would include:

[0047] a. a DNA polymerase

[0048] b. a polynucleotide kinase

[0049] c. a ligase and

[0050] d. a buffer, and optionally the following:

[0051] e. a linearized cloning vector

[0052] f. competent cells

[0053] g. dNTPs

[0054] h. PCR buffer

[0055] i. Taq DNA polymerase or other thermostable DNA polymerase

[0056] One or more control reactions may also be included in the cloningkit. The first three listed enzymes could be combined into a mixture.

[0057] A typical cloning kit is as follows:

[0058] Sticky RICE Enzyme mix (1 U T4 DNA polymerase; 1 U T4Polynucleotide kinase; 0.25 U T4 DNA ligase)

[0059] Sticky RICE buffer mix

[0060] Linearized cloning vector

[0061] Competent Cells

[0062] Control primers

[0063] Control template

[0064] dNTPS

[0065] PCR Buffer

[0066] Taq DNA polymerase

[0067] 2 control reactions.

[0068] The present invention also allows for the generation of a fullyautomated or nearly fully automated cloning system. By using roboticliquid handlers, etc. an automated workflow for cloning PCR productsinto a plasmid vector capable of replicating in a bacterial cell (forexample) could be set up:

[0069] Step 1—set up PCR reactions to amplify up polynucleotidesequences of interest.

[0070] Step 2—analyze PCR reactions on gel, destroy template (ifdesired), purify PCR product away from unincorporated dNTPs. EstimateDNA concentration of purified PCR products.

[0071] Step 3—set up Sticky RICE cloning reactions by combining StickyRICE compatible vector with specific amounts of various PCR products.

[0072] Step 4. let Sticky RICE reaction proceed for appropriate lengthof time.

[0073] Step 5. transform all or a portion of Sticky RICE reaction intobacterial cells.

[0074] Step 6 plate bacteria, pick colonies, prep up DNA from colonies,or cultures thereof, continue with recombinant DNA in experiments asdesired.

[0075] In another embodiment the generation of linear expressionelements for gene discovery/functional genomics experiments, two hybridinteraction experiments, etc. without cloning genes (without propagatingthe recombinant DNA in cells, for example) can be accomplished with thepresent process. This work flow would be as follows and could beautomated as well:

[0076] Step 1—set up PCR reactions to amplify up polynucleotidesequences of interest.

[0077] Step 2—analyze PCR reactions on gel, destroy template (ifdesired), purify PCR product away from unincorporated dNTPs. EstimateDNA concentration of purified PCR product.

[0078] Step 3—set up Sticky Rice cloning reactions by combining StickyRICE compatible polynucleotide elements to 5′ and/or 3′ ends of PCRproducts. These “elements” (described in Step 3) would generally be PCRproducts of polynucleotide sequences with specific useful features suchas: promoters, 5′ untranslated leader sequences, poly adenylationsignals, transcription terminators, stop codons, or open reading frames(ORFs) that could be ligated to a PCR product in frame with the ORF ofthe PCR product—this would allow the production of fusion proteins ateither N or C terminus. Desirable proteins for this application wouldinclude Green fluorescent protein (GFP), polyhistidine (His) tagsequences, cellulose binding domains, streptavidin binding peptidesequences, epitope tags, etc. These fusions would be useful fordetection of the recombinant protein, and/or aid in its purificationand/or detection, etc.

[0079] Step 4: after attaching “elements” of interest to 5′ and/or 3′end of your PCR product, an additional PCR step (to amplify up more ofthe newly constructed recombinant DNA) may be desired.

[0080] Step 5. clean up DNA as needed.

[0081] Step 6: use linear expression element in either in vitro or invivo settings for transcription and/or translation of DNA of interest.For example, linear expression elements can be transfected intomammalian cells and be expressed transiently. Additionally, PCR productscould be transcribed and translated in vitro using commerciallyavailable systems (Promega Corp, Ambion Corp, etc.).

[0082] The advantages of the present Sticky RICE process are flexibilityand speed. In hours one can PCR up more of a DNA of interest forimmediate use. In contrast, it takes days to transfect DNA intobacteria, let the bacteria grow, then purify recombinant DNA frombacterial culture. Also the original PCR product can be modified indifferent ways as desired, providing flexibility in expressing native orfusion proteins in vivo or in vitro.

[0083] The following is a first embodiment of a kit with instructionsfor using STICKY RICE™:

[0084] STICKY RICE™ DNA Cloning kit.

[0085] For Directional Cloning of PCR products into Plasmids

[0086] Kit Contents and Materials List

[0087] Introduction

[0088] Overview

[0089] Experimental Outline

[0090] Methods

[0091] Primer Design for STICKY RICE

[0092] PCR Amplification of DNAs

[0093] Post-PCR Clean up of DNAs

[0094] STICKY RICE™ Ligation Reaction Protocol

[0095] Transformation of competent E. coli cells

[0096] Analysis of transformants

[0097] Troubleshooting and Control Reactions

[0098] Technical Assistance

[0099] Contact information

[0100] Appendix

[0101] Kit Contents and Materials List

[0102] Kit Contents

[0103] The STICKY RICE™ Cloning kit contains the following reagents:Item Contents Amount Control Insert DNA 3 ng/ul 725 bp DNA 25 ul STICKYRICE ™ Prepared ˜10 ng/ul 40 ul Vector (pLSB 1200.bsr) Sterile WaterdH₂O 500 ul  5X STICKY RICE ™ Buffer 5X buffer 50 ul STICKY RICE ™10Xenzyme mix 30 ul Enzyme Mix Control PCR Template 10 ng/ul 20 ulControl Primer set 1 50 uM (each) 20 ul Forward and Reverse primer mix.

[0104] Store all kit components at −20° C.

[0105] Note: Control insert is GFPc3 ORF and will be cloned in framewith the N-terminal His-Patch thioredoxin ORF and C-terminal V5, 6×HisORF in pLSB1200.bsr.

[0106] Materials Supplied by the User

[0107] Thermocycler (PCR) machine.

[0108] Gene Specific Primers

[0109] PCR reagents

[0110] PCR Clean up kit (Stratagene, Qiagen, etc.)

[0111] Competent Bacteria Cells (we recommend MaxEfficiency chemicallycompetent DH5α)

[0112] Introduction

[0113] Overview:

[0114] This kit is designed to let you rapidly clone PCR products in adirectional orientation into the bacterial expression vector pLSB1200.bsr without the use of restriction enzymes. The vector is providedis ready to use, along with all other necessary reagents for the cloningreaction. The kit contains all the components needed to perform 10independent cloning reactions. The Instant RICE Enzyme Mix providedallows for cloning of DNAs at room temperature (22° C.) in 30 minutes.Following the STICKY RICE reaction the DNA is transformed intochemically competent E. coli cells. Approximately 95% of thetransformants should contain inserts in the proper orientation.

[0115] The prepared pLSB 1200.bsr vector provided is a bacterialexpression vector with the following features:

[0116] i T7 lac promoter for high level-inducible expression of the geneof interest.

[0117] ii. LacI gene encoding the lac repressor to tightly regulate geneexpression.

[0118] iii. Ampicillin resistance for selection in E. coli

[0119] iv. pBR322 origin for low-copy replication and maintenance in E.coli.

[0120] v. Directional STICKY RICE™ compatable cloning sites.

[0121] vi. N-terminal His-Patch thioredoxin fusion protein production.

[0122] vii. C-terminal V5 6X His fusion, if desired.

[0123] To clone a gene of interest into pLSB 1200.bsr, the gene issimply amplified up by the polymerase chain reaction (PCR) and the PCRreaction product purified away from unincorporated nucleotides andprimers. The cleaned up PCR product is then combined with STICKY RICEvector, buffer and enzyme mix.

[0124] If the PCR product is inserted in the proper orientation in pLSB1200.bsr, a StuI site will be generated at the upstream vector:insertjunction and a HindIII site will be generated at the 3′ Insert:vectorjunction. This provides an efficient way to screen for the presence andsize of an insert

[0125] Introduction

[0126] Methods

[0127] For efficient, directional joining of PCR products minor primerdesign constraints are necessary. The basic steps of the presentinvention described below are depicted in FIG. 11 and described below:

[0128] 1. Design Primers:

Forward Primer Design

[0129] The forward primer of your gene of interest must have thefollowing 5′ terminal sequence:

[0130] 5′ ggC CTT X₁X₂X₃ XXX XXX

[0131]  Where X₁X₂X₃ is the first codon of your gene of interest. These6 nucleotides (5′ggCCTT) ensure that your gene of interest is cloned inframe with the upstream Thioredoxin gene.

Reverse Primer Design

[0132] The reverse primer of your gene of interest must have thefollowing 5′ terminal sequence (of 4 nts): Gene Sequence: XXX XXXX₁X₁₁X_(iii) Primer Sequence X′X′X′X′X′X′X′X′X′TTC g 5′

[0133] Where X_(i)X_(ii)X_(iii) is a codon of the gene of interest andX′ is a nucleotide base complementary to X. NOTE: if X_(i)X_(ii)X_(iii)is NOT a stop codon, then the gene will be cloned in frame with thedownstream V5-6×His orf, resulting in a C-terminal V5-6XHis fusion toyour protein.

[0134] 2. PCR Amplification of DNAs using properly designed primers

[0135] Set up a 100 ul PCR reaction using the following guidelines:

[0136] Follow manufacturer's recommendations.

[0137] Use the cycling parameters suitable for your primers andtemplate.

[0138] Use a 7 minute final extension time to ensure that all PCRproducts are completely extended.

[0139] After cycling, place the tube on ice or at −20C and proceed toChecking the PCR product, below.

[0140] Checking the PCR Product

[0141] Remove 5 ul from each PCR reaction and use agarose gelelectrophoresis to verify the quality and quantity of your PCR product.Check for the following:

[0142] Be sure you have a single, discrete band of the correct size. Ifyou do not have a single, discrete band, follow the manufacturer'srecommendations for optimizing your PCR with the polymerase of yourchoice. Alternatively, you may gel-purify the desired product using thekit or method of your choice. We have successfully used Stratagene buthave not tested other manufacturers.

[0143] Proceed to Post-PCR Clean up step.

[0144] Post-PCR Clean-Up of DNAs

[0145] a. Prior to cleaning up your PCR product, it is recommended youdestroy the PCR template. To do this add 20 units DpnI restrictionenzyme to your 100 ul PCR reaction. (DpnI is active in PCR buffer.)Digest template for 1 hour at 37° C. Then proceed to step b, below.

[0146] b. Purify your PCR product away from unincorporated dNTPs andprimers using a DNA clean up kit from the manufacturer of your choice.

[0147] Suitable kit manufacturers include: Stratagene PCR clean up kit,Qiaquick PCR clean up kit. (We have not yet tried other manufacturerskits).

[0148] Follow manufacturers instructions and elute final DNA product insterile dH₂O or 10 mM Tris pH 8.0.

[0149] Estimation of DNA Concentration

[0150] Estimation of the cleaned up PCR product DNA concentration can bedone by agarose gel electrophoresis or UV absorption analysis.

[0151] Dilute (or concentrate) your cleaned up PCR product as needed.The recommended amounts of PCR product per STICKY RICE Cloning reactionis 0.015 pmoles. See Step 3, below for more details.

[0152] 3. STICKY RICE™ Ligation Reaction Protocol

[0153] Assemble the STICKY RICE™ Ligation Reaction as follows:

[0154] 2 ul 5× Reaction buffer

[0155] 2 ul STICKY RICE™ Vector DNA (110 ng/ul)

[0156] y ul PCR product (0.015 pmoles insert DNA 2)

[0157] 1 ul STICKY RICE™ Enzyme MIX (add last)

[0158] volume to 10 ul with sterile water.

[0159] Mix gently by pipetting up and down.

[0160] Incubate reaction for 30 minutes at room temperature.

[0161] Note: Each 10 ul STICKY RICE™ Ligation reaction contains ˜20 ng,or 0.005?pmoles, of prepared vector. It is recommended you use 0.015pmoles of insert per reaction. Use the table below to determine theamount of DNA (in nanograms) you need to add depending upon the size ofthe DNA fragment to be cloned. (In general multiply the insert size (inkb) by 10 to determine the number of nanograms needed per 10 ul STICKYRICE™ Ligation reaction. PCR Product Size 0.015 pmoles 0.1 kb  1 ng 0.5kb  5 ng 0.75 kb  7.5 ng    1 kb 10 ng 1.5 kb 15 ng   2 kb 20 ng 2.5 kb25 ng   3 kb 30 ng 3.5 kb 35 ng   4 kb 40 ng 4.5 kb 45 ng   5 kb 50 ng5.5 kb 55 ng   6 kb 60 ng 6.5 kb 65 ng

[0162] 4. Transformation of Competent E. coli Cells.

[0163] Thaw competent DH5a chemically competent cells on ice.

[0164] We have used Invitrogen Max Efficiency DH5α, E. coli (>1×10⁹transformation efficiency).

[0165] Place 14 ml polypropylene tube Falcon (35/2059) on ice topre-chill.

[0166] Transfer 35 ul thawed cells to chilled 14 ml polypropylene tube

[0167] Add 1 ul STICKY RICE™ Ligation reaction to competent DH5a cellsin 14 ml tube Swirl gently to mix.

[0168] Incubate on ice 15 min.

[0169] Transfer to 42° C. water bath for 45 seconds.

[0170] Return to ice 2 minutes.

[0171] Add 400 ul 50C media (room temp) to cells.

[0172] Plate 50 or 150 ul per plate onto LB Amp plates (100 ug/mlAmpicillin)

[0173] Incubate plates at 37° C. overnight.

[0174] 5. Analysis of Transformants.

[0175] Using a toothpick, pick and inoculate 2 ml LB (100 ug/mlampicillin) samples with individual colonies. Pick at least 6independent colonies.

[0176] Grow liquid cultures overnight at 37° C. and shaking (300 rpm)

[0177] Prepare DNA from liquid cultures using Qiagen plasmid DNAminiprep kit.

[0178] Screen plasmids for inserts by digestion with StuI and HindIII.

[0179] We recommend digesting 2 ul of miniprep DNA in a 15 ul reactioncontaining 0.5 ul (each) of StuI and HindIII restriction enzymes. Digestfor 1 hour at 37C.

[0180] Run restriction enzyme digested samples on 1% agarose gel toanalyze.

[0181] After the StuI-HindIII digest, the pLSB 1200.bsr vector will beapproximately 6.3 kb in length. Any additional fragments will be due toyour insert.

[0182] 6. Expression of Protein in E. coli from pLSB1200.bsr Vector.

[0183] Transform plasmid DNA from isolates of interest into E. coli BL21DE3 cells (Invitrogen) as per manufacturers instructions. To produceprotein in E. coli follow instructions for induction and expression ofprotein(s).

[0184] Troubleshooting and Control Reactions:

[0185] The STICKY RICE™ reaction components and protocol are designed tomaximize specific, directional joining of PCR products, while minimizingthe amount of non-specific, non-directional joining of PCR products.Several elements contribute to this specificity, including:

[0186] 1. DNA concentration.

[0187] High concentrations of DNA facilitate blunt DNA ligationreactions. Increasing the DNA concentration above the amountsrecommended in this manual may lead to non-specific (blunt) joining ofPCR products.

[0188] 2. Enzyme concentration.

[0189] The STICKY RICE™ Enzyme Mix is specially formulated to limit theamount of non-specific joining of PCR fragments.

[0190] Appendix:

[0191] Appendix Table of Contents:

[0192] Control Primer Sequences:

[0193] Reagents and Supplies list

[0194] STICKY RICE™ Buffer recipe

[0195] STICKY RICE™ Enzyme mix recipe

[0196] Preparation of Vector

[0197] Preparation of Control Insert

[0198] Control STICKY RICE™ Ligation reaction and Results

[0199] Plasmid map of pLSB 1200.bsr

[0200] pLSB 1200.bsr cloning sites

[0201] Control Primer Sequences

[0202] Forward primer Seq ID NO: 3: ggC CTT ATg gCT AgC AAA ggA gAA gAAC (IDT Inc. Coralville, Iowa)

[0203] Reverse primer Seq ID NO: 4: gCT TgT AgA gCT CAT CCA TgC CAT g(IDT Inc. Coralville, Iowa)

[0204] Control PCR template: GFPc3 ORF in pUC-based cloning vector.

[0205] Reagents and Supplies List:

[0206] DNA purification Reagents:

[0207] Successful results have been obtained with the following kits.

[0208] QIAGEN plasmid DNA prep system

[0209] Stratagene plasmid DNA prep system

[0210] Stratagene PCR clean up kit.

[0211] Zymoclean Gel Purification kit.

[0212] Restriction Enzymes

[0213] New England Biolabs (NEB) Sap I (Cat # R0569) 2 U/ul

[0214] NEB SnaB I (Cat # R0130) 5 U/ul

[0215] NEB Hind III (Cat # R0104) 20U/ul

[0216] NEB Stu I (Cat # R0187) 10U/ul

[0217] NEB Dpn I (Cat # R0176) 20U/ul

[0218] DNA Modification Enzymes:

[0219] T4 DNA polymerase. Novagen LIC qualified (Cat #70099-3) 2.5U/ul

[0220] T4 polynucleotide kinase: NEB (Cat #M0201) 10 U/ul

[0221] T4 DNA ligase (Invitrogen Cat # 15224-017) 1U/ul

[0222] dNTPs

[0223] Promega (Cat #U1330) set of 4 individual dNTPs each at 100 mM

[0224] Buffers:

[0225] NEB Restriction enzyme buffers 2 and 4

[0226] NEB T4 DNA ligase buffer

[0227] Composition of 10×buffer:

[0228] 500 mM Tris-HCl (pH 7.5)

[0229] 100 mM MgCl₂

[0230] 100 mM DTT

[0231] 10 mM rATP

[0232] 250 ug/ml BSA

[0233] PCR Reagents:

[0234] Pfu Turbo DNA polymerase. (Stratagene Cat #600250) 2.5 U/ul

[0235] 10× cloned Pfu buffer (Stratagene)

[0236] STICKY RICE™ Buffer Mix:

[0237] 50 ul 2 mM (each) dATP/dTTP

[0238] 50 ul NEB 10×T4 DNA ligase buffer.

[0239] Result: 100 ul of 5×STICKY RICE™ Buffer

[0240] STICKY RICE™ Enzyme Mix:

[0241] 10 ul Novagen T4 DNA pol (2.5U/ul)

[0242] 5 ul NEB T4 polynucleotide kinase (10U/ul)

[0243] 50 ul Gibco (Invitrogen) T4 DNA ligase (1U/ul)

[0244] Result: 65 ul of 10× STICKY RICE™ enzyme mix.

[0245] Preparation of pLSB 1200.bsr Vector for STICKY RICE™ Cloning.

[0246] NOTE: This is HOW the supplied vector has been prepared. A userof the present invention does not need to prepare the supplied vector.

[0247] A. Purify pLSB 1200.bsr vector from DH5a E. coli cultures usingStratagene or QIAGEN plasmid DNA purification systems.

[0248] B. Digest pLSB 1200.bsr vector DNA as follows:

[0249] 10 ul 10×NEB 4 buffer

[0250] 1 ug pLSB 1200.bsr DNA

[0251] 1 ul 100×BSA (NEB)

[0252] 5 ul Sap I Restriction enzyme

[0253] Volume to 100 ul with dH₂O.

[0254] Digest at 37° C. for about 16 hours (ex, 5 pm to 8 am)

[0255] Add 1 ul SapI (2U/ul stock) and 1 ul SnaBI (5 U/ul stock) to 100ul digest

[0256] Return to 37° C. 1 hour.

[0257] C. Purify digested DNA with Stratagene or QIAGEN PCR clean upsystems as per manufacturers instruction with the followingmodification: Perform one extra column wash than suggested by protocol.

[0258] Elute in 50 ul dH20.

[0259] D. Run 2 ul of purified DNA on 1% agarose gel to estimate qualityand/or quantity of DNA.

[0260] Alternatively, record A260/A280 readings of DNA (100 ul of a 1:20dilution) to estimate DNA concentration.

[0261] Adjust cut vector DNA concentration to about 5 ng/ul in dH₂O.

[0262] Store at −20° C.

[0263] Preparation of Control Insert:

[0264] NOTE: This is HOW the supplied control insert has been prepared.A user of the present invention does not need to prepare control insert,unless he so desires.

[0265] Set up a PCR of the (ca. 725 bp) GFP control insert as follows:

[0266] 10 ul 10× cloned Pfu buffer (Stratagene)

[0267] 50 pmoles F primer (SEQ ID NO: 3)*

[0268] 50 pmoles R primer (SEQ ID NO: 4)

[0269] 10 ng template (GFP gene in pUC based plasmid)

[0270] 2 ul dNTP mix (dATP, dTTP, dGTP, dCTP) each at 10 mM

[0271] 2 ul Pfu Turbo DNA Polymerase

[0272] Volume to 100 ul with dH₂O

[0273] 50 pmoles=1 ul of 50 uM stock.

[0274] Cycling conditions (MJ Research PTC 200)

[0275] 1. 95° C. 2 min

[0276] 2. 94° C. 30 sec

[0277] 3. 55° C. 30 sec (steps 2-4 for 25 cycles)

[0278] 4. 72° C. 1 min

[0279] 5. 72° C. 7 min

[0280] 6. 4° C. hold

[0281] Add 20 U Dpn I to PCR reaction when completed.

[0282] Incubate at 37° C. 1 hour (to destroy template DNA)

[0283] Run 2 ul of PCR reaction on 1.5% agarose gel to check.

[0284] Clean up PCR product with Stratagene or QIAGEN PCR clean up kits,according to manufacturers instructions.

[0285] Elute in 50 ul dH₂O

[0286] Run 2 ul cleaned up PCR product on gel to check.

[0287] Record A260/A280 of cleaned up PCR product (1:50 dil) to estimateDNA concentration.

[0288] Adjust concentration of cleaned up PCR product to approximately3-4 ng/ul, for use as test insert. Control STICKY RICE ™ Ligationreaction and Results Reagent Control Lig Test Lig 5X Buffer  2 ul   2 ulVector 10 ng  10 ng Control Insert — 7.5 ng Water up to 9 ul vol up to 9ul vol STICKY RICE ™  1 ul   1 ul Enzyme Mix Final vol 10 ul  10 ul

[0289] Mix gently by pipetting.

[0290] Let incubate at room temp for 30 min.

[0291] Transform 1 ul each reaction into 35 ul DH5a, plate cells etc. asdescribed in protocol.

[0292] Incubate overnight at 37° C.

[0293] Record the number of colonies per plate next day.

[0294] NOTE: A decent vector prep should give about 10×-40× morecolonies on the ligation reaction than on the re-ligation controlreaction. Re-ligation control should have 20-50 colonies, for exampleper 50 ul plated

[0295] Expected results: >or =to 95% of transformants contain plasmidswith inserts.

[0296] The following is a second embodiment of a kit with instructionsfor using STICKY RICE™:

[0297] STICKY RICE™ Linear DNA Recombination Kit.

[0298] For Construction of linear recombinant DNAs in vitro.

[0299] Kit Contents and Materials List

[0300] Introduction

[0301] Overview

[0302] Experimental Outline

[0303] Methods

[0304] Primer Design for STICKY RICE

[0305] PCR Amplification of DNAs

[0306] Post-PCR Clean up of DNAs

[0307] STICKY RICE™ Reaction Protocol

[0308] Gel Analysis of Reaction products

[0309] Troubleshooting and Control Reactions

[0310] Technical Assistance

[0311] PCR Control Reaction

[0312] STICKY RICE Control Reaction

[0313] Appendix

[0314] Recipes

[0315] Technical Service

[0316] References

[0317] Kit Contents and Materials List

[0318] Kit Contents The STICKY RICE™ Linear Recombination kit containsthe following reagents: Item Composition Amount Control DNA-1  8 ng/ul225 bp frag 25 ul Control DNA-2 25 ng/ul 725 bp frag 25 ul Control DNA-310 ng/ul 300 bp frag 25 ul Sterile Water 500 ul  5X STICKY RICE ™ 5Xbuffer 50 ul Buffer STICKY RICE ™ 10Xenzyme mix 30 ul Enzyme Mix ControlTemplate 10 ng/ul 20 ul Control Primer Set 1 50 uM Each primer 20 ulControl Primer Set 2 50 uM Each primer 20 ul Control Primer Set 3 50 uMEach primer 20 ul Primer Seq ID NO: 6 (F) 50 uM Seq ID NO: 6 primer 20ul Primer Seq ID NO: 13 (R) 50 uM Seq ID NO: 13 primer 20 ul

[0319] Materials Supplied by the User

[0320] Thermocycler (PCR) machine

[0321] PCR Reagents

[0322] PCR Clean up kit

[0323] Introduction

Overview

[0324] This kit is designed to let you rapidly join linear DNA (PCR)products in a directional orientation. The STICKY RICE™ Enzyme Mixfacilitates joining of linear DNAs at room temperature (22° C.) in 60minutes. Greater than 50% of the control reaction substrates should bedirectionally joined in a 60 minute STICKY RICE™ joining reaction.

[0325] For efficient, directional joining of PCR products minor primerdesign constraints are necessary (for complete description see Methodssection). The provided control PCR reaction products of 225 (DNA-1) and725 bp (DNA-2) for example, are joined (at their overlapping GCCsequence termini) to generate a product of about 950 bp. See FIG. 12.Alternatively template and primers are provided to allow you to amplifyup these two PCR products for use in control reactions. Instructions forprimer design will allow you to generate your own PCR products for usein a STICKY RICE™ joining procedure. You may also set up a 3 way STICKYRICE™ reaction by adding in equimolar amounts of control DNA-3. Thebasic steps of the method described here are depicted in FIG. 12.

[0326]FIG. 12 depicts the joining of 225 and 725 bp PCR products bySTICKY RICE™. ^(5′) ---225----GCC3′ (DNA-1 in kit) _(3′)----225----CGG5′               ^(5′)GCC----725bp -------^(3′) (DNA-2 in kit)               _(3′)CGG----725bp--------_(5′)5′ -------225bp------GCC--------725 bp-----3′3′-------225bp------CGG--------725 bp-----5′

[0327] The STICKY RICE™ joining procedure is useful for joining PCRproducts for the construction of chimeric genes, gene fusions, or otherlinear recombinant DNAs of interest.

[0328] Introduction

[0329] SEE FIG. 12 for Experimental Steps

[0330] Methods

[0331] Design Primers for STICKY RICE™

[0332] During the STICKY RICE™ Ligation reaction, 5′ complementary(sticky) overhangs are generated and guide the directional assembly ofDNA molecules. The efficiency and rate of the joining reactioncorrelates with the calculated melting temperature of the generated 5′overhangs. The higher the estimated melting temperature of the stickyends, the faster the reaction progress.

[0333] For this reason, G/C rich sticky ends are preferred over A/T richsticky ends, though both types of sticky ends work. The sequence andlength of the 5′ sticky ends to be generated is determined by primerdesign prior to PCR. For example 1f two DNA fragments (left) and (right)are to be joined the following design is suggested. Left Fragment,Reverse primer (5′ GGC W-gene of interest sequence)

EXAMPLE

[0334] DNA Sequence: NNN NNN Primer Sequence: NNN NNN W CGG5′

[0335] where W=A or T

[0336] The forward direction primer for the Left fragment is a genespecific primer.

[0337] Right fragment, forward primer (5′ GCC W-gene of interestsequence)

EXAMPLE

[0338] DNA Sequence: gene of interest--        ATG GGC ATT (Seq ID NO:5)Primer Sequence: 5′ GCC ATG GGC ATT

[0339] Reverse primer for the Right fragment is a gene specific primer.

[0340] PCR Amplification of DNAs

[0341] Set up a 100 μl PCR reaction using the following guidelines:

[0342] Follow manufacturer's recommendations.

[0343] Use the cycling parameters suitable for your primers andtemplate.

[0344] Use a 7 minute final extension time to ensure that all PCRproducts are completely extended.

[0345] It is recommended to set up the control fragments in thefollowing manner: Pfu turbo(2.5 U/ul) 2 μl 10X cloned Pfu buffer 10 μl 10 mM dNTPs 2 μl Control primers set 1 or 2 1 μl control template 2 μlsterile water 83 μl 

[0346] Using an MJ research thermocycler (use of a different PCR machinewill require optimization of the cycling conditions), the reaction isheated to 95° C. for 2 minutes then cycled for 25 times through thefollowing three temperatures: 95° C., 30 seconds; 55° C., 30 seconds;72° C. 1 minute. After the final cycle, the reaction is incubated at 72°C. for 7 minutes and then held constant at 4° C. until ready for nextstep.

[0347] After cycling, place the tube on ice or at −20C and proceed toChecking the PCR product, below.

[0348] Checking the PCR Product

[0349] Remove 2-5 ul from each PCR reaction and use agarose gelelectrophoresis to verify the quality and quantity of your PCR product.Check for the following:

[0350] Be sure you have a single, discrete band of the correct size. Ifyou do not have a single, discrete band, follow the manufacturer'srecommendations for optimizing your PCR with the polymerase of yourchoice. Alternatively, you may gel-purify the desired product using themethod of your choice. We have used Stratagene based kits

[0351] Proceed to Post-PCR Clean up step.

[0352] Post-PCR Clean-Up of DNAs

[0353] Before cleaning up PCR fragments, add 20 units DpnI per 100 ulreaction to remove template background. Incubate DpnI treated sample for1 hour at 37 degrees celcius. Heat kill enzyme for 20 minutes at 80degrees celcius. Proceed with purification of PCR products.

[0354] Purify your PCR product away from unincorporated dNTPs andprimers using a DNA clean up kit from the manufacturer of your choice.

[0355] Suitable kit manufacturers include: Stratagene PCR clean up kit,Qiaquick PCR clean up kit.

[0356] Follow manufacturers instructions and elute final DNA product insterile dH₂O

[0357] Estimation of DNA Concentration

[0358] Estimation of the cleaned up PCR product DNA concentration can bedone by agarose gel electrophoresis or UV absorption analysis.

[0359] Dilute (or concentrate) your cleaned up PCR product as needed.The recommended amounts of PCR products per STICKY RICE™ joiningreaction are approximately 0.05 pmoles each fragment per 15 ul reaction(for 2-way ligation reactions). When joining two PCR products equimolaramounts of each PCR product are recommended. For 3-way ligations, it isrecommended that the middle fragment be in excess of the other twofragments. A 1:3:1 molar ratio is recommended-0.025 pmoles of eachoutside fragment and 0.075 pmols of the inside fragment.

[0360] Control PCR products of 225 bp, 725 bp and 300 bp are suppliedwith the kit at 8 ng, 25 ng, and 10 ng/ul respecitively. One microliterof each fragment is 0.05 pmoles.

[0361] 3. Set up STICKY RICE™ Ligation Reaction.

[0362] Assemble the STICKY RICE™ Reaction as follows:

[0363] 3 ul 5× Reaction buffer

[0364] x ul DNA 1 (0.05 pmoles DNA 1 or 1 μl of control DNA-1)

[0365] y ul DNA 2 (0.05 pmoles DNA 2 or 1 μl of control DNA-2)

[0366] 1 ul STICKY RICE™ Enzyme Mix (added last) volume to 15 ul withsterile water.

[0367] Mix by pipetting up and down gently or vortexing very gently

[0368] Incubate reaction for 60 minutes at room temperature (22° C.).

[0369] NOTE: Alternatively, if you wish to try a 3-way STICKY RICE™Ligation Reaction, add 0.025 pmoles (0.5 μl of DNA-1 and DNA-3) of the225 bp and 300 bp (provided) and 0.075 pmoles of (1.5 ul of DNA-2) tothe above recipe and make adjustments accordingly to the amount of wateradded to the reaction. In the 3 way STICKY RICE™ Ligation the finalproduct will be approximately 1300 bp in length. The fragments shouldassemble in the following orientation:

[0370] DNA1 (225 bp): DNA2 (725 bp): DNA3 (300 bp) TABLE 1 Amount of DNA(in nanograms) 0.05 pmoles PCR Product Size 0.05 pmoles 0.1 kb 3.3 ng 0.5 kb 16 ng 0.75 kb  25 ng   1 kb 33 ng 1.5 kb 50 ng   2 kb 66 ng 2.5kb 83 ng   3 kb 99 ng

[0371] 4. Gel Analysis of Reaction

[0372] Stop Reaction:

[0373] Incubate the STICKY RICE™ Ligation Reaction at 75° C. for 15minutes. This step is important to ensure you will have sharp bands onyour gel.

[0374] Use agarose gel electrophoresis to examine the progress of eachSTICKY RICE™ Reaction. Run 10 ul of STICKY RICE Ligation Reaction on theappropriate concentration agarose gel, with the appropriate DNA sizemarkers. Stain with EtBr and visualize fragments with UV illumination.

[0375] For the control reaction provided with this kit, a 1.5% agarosegel is recommended for the analysis of the control reaction. The usershould see a 225 and 725 bp band in addition to a 950 bp band from thejoining of control DNAs 1 and 2.

[0376] 5. Linear Recombinant for use in your Application of Interest.

[0377] If desired, you may wish to PCR amplify up the assembled 1.3 kbrecombinant TM DNA from the 3 way STICKY RICE™. To do this, use oligosSeq ID NO: 15 (225 F) and Seq ID NO: 13 and 1 ul of your STICKY RICE™ligation reaction in the following PCR set-up Pfu turbo (2.5 U/ul) 2 μl10X cloned Pfu buffer 10 μl  10 mM dNTPs 2 μl 50 μM Seq ID NO: 15 1 μl50 μM Seq ID NO: 13 1 μl ligation product 1 μl sterile water 83 μl 

[0378] Using an MJ research thermocycler (use of a different PCR machinewill require optimization of the cycling conditions), the reaction isheated to 95° C. for 2 minutes then cycled for 20-25 times through thefollowing three temperatures: 95° C., 30 seconds; 50° C., 30 seconds;72° C. 1 minute, 30 seconds. After the final cycle, the reaction isincubated at 72° C. for 7 minutes and then held constant at 4° C. untilready for next step. Check 2 ul on a 1.2-1.5% agarose gel. You shouldonly see the ligation product band as a result of PCR.

[0379] Troubleshooting and Control Reactions:

[0380] The STICKY RICE™ reaction components and protocol are designed tomaximize specific, directional joining of PCR products, while minimizingthe amount of non-specific, non-directional joining of PCR products.Several elements contribute to this specificity, including:

[0381] 1. DNA concentration.

[0382] High concentrations of DNA facilitate blunt DNA ligationreactions.

[0383] Increasing the DNA concentration above the amounts recommended inthis manual may lead to non-specific (blunt) joining of PCR products.

[0384] 2. Enzyme concentration.

[0385] The Instant RICE™ Enzyme Mix is specially formulated to limit theamount of non-specific joining of PCR fragments.

[0386] 3. Primer design.

[0387] Palidromic sticky ends can lead to non-directional annealing andjoining of DNA fragments. To ensure that joining is directional designyour primers so that non-palindromic sticky 5′ overhangs will result.

[0388] Appendix:

[0389] Primer pairs for 3 way STICKY RICE™ PCR products: 225 bp PCRproduct: (from pUC:GFP template)   F primer (Seq ID NO: 6) 5′ gac tcttca agc gca aga gcg ccc aat acg ca 3′   R primer (Seq ID NO: 7) 5′ ggctta gct gtt tcc tgt gtg aaa ttg tt 3′ 225 bp fragment sequence:GACTCTTCAAGCGCAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTC (Seq IDNO: 8) ATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTAAGCC 725 bp PCR product(from pUC:GFP template)   F primer (Seq ID NO: 9) 5′ gcc atg gct agc aaagga gaa gaa c 3′   R primer (Seq ID NO: 10) 5′ cgg tta ttt gta gag ctcatc cat gcc a 3′ 726 bp fragment sequence:GCCATGGCTAGCAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGA (Seq IDN): 11) TGGTGATGTTAATGGGCACAAATTTTCTGTCAGTGGAGAGGGTGAAGGTGATGCTACATACGGAAAGCTTACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCATGGCCAACACTTGTCACTACTTTCTCTTATGGTGTTCAATGCTTTTCCCGTTATCCGGATCATATGAAACGGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAACGCACTATATCTTTCAAAGATGACGGGAACTACAAGACGCGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTTAATCGTATCGAGTTAAAAGGTATTGATTTTAAAGAAGATGGAAACATTCTCGGACACAAACTCGAGTACAACTATAACTCACACAATGTATACATCACGGCAGACAAACAAAAGAATGGAATCAAAGCTAACTTCAAAATTCGCCACAACATTGAAGATGGATCCGTTCAACTAGCAGACCATTATCAACAAAATACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCGACACAATCTGCCCTTTCGAAAGATCCCAACGAAAAGCGTGACCACATGGGCCTTCTTGAGTTTGTAACTGCTGCTGGGATTACACATGGCATGGATGAGCTCTACAAATAACCG 300 bp PCR product (frompUC:GFP template DNA)   F primer (Seq ID NO: 12) 5′ ccg ttt taa gcc agcccc gac cac ccg cca 3′   R primer (Seq ID NO: 13) 5′ gat gag cgg ata catatt tga atg 3′ 300 bp fragment sequence:CCGTTTTAAGCCAGCCCCGACACCCGCCAACACCCGCTGACGCGCCCTGACGGGCTTGTCTG (Seq IDNO: 14) CTCCCGGCATCCGCTTACAGACAAGCTGTGACCGTCTCCGGGAGCTGCATGTGTCAGAGGTTTTCACCGTCATCACCGAAACGCGCGAGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATC

EXAMPLES

[0390] The following examples illustrate the practice of the presentinvention but should not be construed as limiting its scope.

Example 1 Preparation of Oligos

[0391] The oligonucleotides listed in Table 1 below were prepared foruse in the following examples. TABLE 1 Oligonucleotides SEQ ID NO: 15gac tct tca agc gca aga gcg ccc aat acg ca SEQ ID NO: 16 AAT ggC TAg CAAAgg AgA AgA AC SEQ ID NO: 17 TAA ggT TAT TTg Tag AgC TCA TCC ATg C SEQID NO: 18 ATT ggT AgC TgT TTC CTg TgT gAA ATT gT SEQ ID NO: 19 TTA ggTTAA gCC AgC CCC gAC ACC CgC CA SEQ ID NO: 20 ggC ATg gCT AgC AAA ggA gAAgAA C SEQ ID NO: 21 Cgg TTA TTT gTA gAg CTC ATC CAT gCC A SEQ ID NO: 22gCC TTA gCT gTT TCC TgT gTg AAA TTg TT SEQ ID NO: 23 CCg TTT TAA gCC AgCCCC gAC ACC CgC CA SEQ ID NO: 24 AAA ATg gCT AgC AAA ggA gAA gAA C SEQID NO: 25 TTA ggT TAT TTg Tag AgC TCA TCC ATg CC SEQ ID NO: 26 ATT TTCgAg CTg TTT CCT gTg TgA AAT Tg SEQ ID NO: 27 TAA CCT TAA gCC AgC CCC gACACC CgC CA SEQ ID NO: 28 CCA Tgg CTA gCA AAg gAg AAg AAC SEQ ID NO: 29gCC TTA TTT gTA gAg CTC ATC CAT gCC AT SEQ ID NO: 30 ggT TAg CTg TTT CCTgTg TgA AAT TgT T SEQ ID NO: 31 ggC TTT TAA gCC AgC CCC gAC ACC CgC CA

Example 1A Ligation of Two Linear DNAs (PCR Reaction Products) by StickyRICE

[0392] A 225 bp fragment of pUC 19 was amplified by the PCR using oligosSeq ID NO: 15 and Seq ID NO: 18, in a 100 ul reaction containing 1×TaqDNA polymerase buffer with MgCl2 (Promega), 100 pmoles each oligo, 0.2mM final concentration of each dNTP (dGTP, dCTP, dATP, dTTP), 50 pg pUC19 (Invitrogen) and 5U Taq DNA polymerase (Promega catalog # Ml 661).The reaction was heated to 94° C. for 3 minutes then cycled for 30 timesthrough the following three temperatures: 94° C., 15 sec; 50° C. 30 sec;72° C. 20 sec. After the final cycle, the reaction was incubated at 72°C. for 5 minutes.

[0393] A 770 bp DNA fragment of the GFP gene was amplified from theplasmid p30BGFPc3 (Shivprasad S., Pogue, G P, Lewandowski D J, HidalgoJ, Donson J, Grill L K, Dawson W O. 1999. Heterologous sequences greatlyaffect foreign gene expression in tobacco mosaic virus-based vectors.Virology 255(2) 312-323.) by the PCR using oligos Seq ID NO: 16 and SeqID NO: 17, in a 100 ul reaction containing 1×Taq DNA polymerase bufferwith MgCl2 (Promega), 100 pmoles each oligo, 0.2 mM final concentrationof each dNTP (dGTP, dCTP, dATP, dTTP), and 5U Taq DNA polymerase(Promega catalog #M1661). The reaction was heated to 94° C. for 3minutes then cycled for 30 times through the following threetemperatures: 94° C., 20 sec; 50° C. 30 sec; 72° C. 45 sec. After thefinal cycle, the reaction was incubated at 72° C. for 5 minutes.

[0394] Following PCR the PCR products were purified from unincorporateddNTPs, oligonucleotides, buffer, etc using the StrataPrep PCRpurification kit (Stratagene) using the manufacturers instructions. Thepurified PCR products were eluted from StrataPrep columns with dH₂O.

[0395] Approximately 50 ng of the two purified PCR reaction productswere combined in a 10 ul reaction containing: 1× New England Biolabs(NEB) ligase buffer, 1.25 U T4 DNA pol (Novagen, LIC qualified), and 0.2mM (each) dGTP and dCTP. The reaction was incubated at 37° C. for 30minutes. Following the 37° C. treatment 0.5 ul of a mixture of0.2Units/ul Gibco T4 DNA ligase and 1 Unit/ul T4 polynucleotide kinase(Novagen) in 1×NEB ligase buffer was added, the reaction mixed bypipetting. The reaction was then allowed to proceed for approximately 1hour at room temperature.

[0396] The T4 DNA polymerase and dNTP treatment generated 5′ overhangson the two PCR products as described in the table below: !225 bp PCRProduct? 770 bp PCR Product PCR primers 308-351 349-350 used ds PCR prod5′gac tct--------cc aat 5′aat ggc-----------acc tta   ctg aga--------ggtta   tta ccg-----------tgg aat Post T4 pol treat 5′gac tct----------cc5′aat ggc-----------acc with dGTP/dCTP   ctg aga----------gg tta      ccg-----------tgg aat

[0397] The 5′ overhangs of the two polynucleotides in bold arecomplementary to each other.

[0398] After incubating at room temperature, the reaction was analyzedby electrophoresis through a 2% Agarose gel in 1×TAE buffer, stainedwith EtBr and photographed under UV light.

Example 1B:

[0399] Example 1B was performed using the substantially the sameprocedures of Example 1A with the following exceptions: The 225 bpproduct from pUC 19 was generated with oligos Seq ID NO: 15 and Seq IDNO: 22. The 770 bp product (GFP gene) was amplified with PCR primers SeqID NO: 20 and Seq ID NO: 21. And the T4 DNA polymerase treatmentcontained 0.2 mM (each) dATP and dTTP, in place of dGTP and dCTP.

[0400] The T4 DNA polymerase and dNTP treatment generated 5′ overhangson the two PCR products as described in the table below: !225 bp PCRProduct? 770 bp PCR Product PCR primers 308-355 353-354 used ds PCR prod5′gac tct---------taa ggc 5′ggc atg---------taa ccg   ctgaga---------att ccg   ccg tac---------att ggc Post T4 pol treat 5′gactct----------taa 5′ggc atg---------taa with dATP/dTTP   tgaga----------att ccg       tac--------att ggc

[0401] The 5′ overhangs of the two polynucleotides in bold arecomplementary to each other.

[0402] After incubating at room temperature, the reaction was analyzedby electrophoresis through a 2% Agarose gel in 1×TAE buffer, stainedwith EtBr and photographed under UV light.

Example 1C

[0403] Example 1C was performed using substantially the same proceduresof Example 1A with the following exceptions: The 225 bp product from pUC19 was generated with oligos Seq ID NO: 15 and Seq ID NO: 26. The 770 bpproduct (GFP gene) was amplified with PCR primers Seq ID NO: 24 and SeqID NO: 25

[0404] The T4 DNA polymerase and dNTP treatment generated 5′ overhangson the two PCR products as described in the table below: 225 bp PCRProduct 770 bp PCR Product PCR primers used 308-359 357-358 Ds PCR prod5′gac tct----------gaa aat 5′aaa atg g--------acc taa   ctgaga----------ctt tta   ttt tac c--------tgg att Post T4 pol treat 5′gactct----------g 5′aaa atg g-------acc with dGTP/dCTP   ctgaga----------ctt tta         c c-------tgg att

[0405] The 5′ overhangs in bold will be complementary to each other.

[0406] After incubating at room temperature, the reaction was analyzedby electrophoresis through a 2% Agarose gel in 1×TAE buffer, stainedwith EtBr and photographed under UV light.

Example 1D

[0407] Example 1D was performed using substantially the same proceduresof Example 1B with the following exceptions: The 225 bp product from pUC19 was generated with oligos Seq ID NO: 15 and Seq ID NO: 30. The 770 bpproduct (GFP gene) was amplified with PCR primers Seq ID NO: 28 and SeqID NO: 29.

[0408] The T4 DNA polymerase and dNTP treatment generated 5′ overhangson the two PCR products as described in the table below: 225 bp PCRProduct 770 bp PCR Product PCR primers used 308/363 361-362 ds PCR prod5′gac tct----------aa cc 5′cc atg---------taa ggc   ctg aga----------ttgg   gg tac---------att ccg Post T4 pol treat 5′gac tct----------aa 5′ccatg---------taa with dATP/dTTP   tg aga----------tt gg     tac---------att ccg

[0409] The 5′ overhangs of the two polynucleotides in bold arecomplementary to each other.

[0410] After incubating at room temperature, the reaction was analyzedby electrophoresis through a 2% Agarose gel in 1×TAE buffer, stainedwith EtBr and photographed under UV light.

[0411] Results of Examples 1A-1D:

[0412] In each of the examples 1A-1D (depicted in FIG. 1), the desiredresult would be for the ligation of the 225 and 770 bp products togenerate a DNA fragment of about 1000 bp in size. In FIG. 1, Lane1=Promega 100 bp DNA molecular weight ladder; lane 2=Ex 1A reaction,lane 3=Ex 1B reaction; lane 4=Ex 1C reaction; lane 5=Ex 1D reaction.

[0413]FIG. 1 is a photograph of a gel that shows the relative efficiencyof ligation under these conditions and is as follows: B=C>D>>A. Therelative ligation efficiency in this experiment paralleled thecalculated melting temperature (Tm) for the predicted sticky ends, usingthe formula Tm=2(A/T)+4 (G/C), where Tm is in degrees C. Using thisformula the predicted Tms for the various sticky ends are: Ex 1B (12°C.), Ex 1C (10° C.), Ex 1D (8° C.), Ex 1A (6° C.).

[0414] If desired the ligation reaction step of the sticky RICE reactioncan be performed at 16° C. and/or for extended periods of time toincrease the final yield of ligated product.

Example 2 Construction of a Recombinant Plasmid Using Sticky RICE

[0415] Vector Preparation.

[0416] Several modifications of pUC 19 were generated using thepolymerase chain reaction. Primer pairs were designed so that an“inverse PCR” reaction of the pUC 19 DNA template would generate a dsDNA of about 2.6 kb in size. The 5′ end of one primer of each pair willsit just upstream of the ATG start codon of the lac alpha peptide ORF,with its 3′ end proximal to the Lac promoter. The 5′ end of the otherprimer of each pair will sit just downstream of the stop codon of thelac alpha peptide with the 3′ end proximal to the promoter for theampicillin resistance gene. FIG. 2 shows the plasmid pUC 19 and therelative locations and directions of the primers used for amplificationof pUC 19 by PCR for experiments 2A-2D. Primers are represented by thesolid arrows, 5′ (blunt end of arrow) to 3′ (point of arrow). Primers(Seq ID NOS:) 18, 22, 26 and 30 hybridize to pUC 19 at the locationidentified by primer B in FIG. 2. Primers (Seq ID NOS:) 19, 23, 27 and31 hybridize to pUC 19 at the location identified by primer A in FIG. 2.

[0417] Specifically, FIG. 2 shows the plasmid pUC 19 and the relativelocations and directions of the primers used for amplification of pUC 19by PCR for experiments 2A-2D. Primers are represented by the solidarrows, 5′ prime (blunt end of arrow) to 3 prime (point of arrow).Primers (Seq ID NOS:) 18, 22, 26 and 30 hybridize to pUC 19 at thelocation identified by primer B in figure above. Primers (Seq ID NOS:)19, 23, 27 and 31 hybridize to pUC 19 at the location identified byprimer A in FIG. 2.

[0418] The pUC 19 plasmid was amplified by the PCR using oligos Seq IDNO: 18 and Seq ID NO: 19, in a 100 ul reaction using the 1×bufferdescribed by Barnes (Barnes WM. 1994. PCR amplification of up to 35 kBDNA with high fidelity and high yield from lambda bacteriophagetemplates. PNAS 91(6) 2216-20). 100 pmoles each oligo, 0.2 mM finalconcentration of each dNTP (dGTP, dCTP, dATP, dTTP), 100 pg pUC 19(Invitrogen) and 3.5U Taq DNA polymerase (Promega catalog # M1661) and0.035 Units Pfu Turbo DNA polymerase (Stratagene) were combined to forma reaction mixture. The reaction was heated to 94° C. for 3 minutes thencycled for 30 times through the following three temperatures: 94° C., 30sec; 50° C. imin; 72° C. 3 min. After the final cycle, the reaction wasincubated at 72° C. for 5 minutes.

[0419] Separate PCR reactions of pUC 19 DNA template were set up asabove, using the following primer pairs: SEQ ID NO: 22 and SEQ ID NO:23; SEQ ID NO: 26 and SEQ ID NO: 27; SEQ ID NO: 30 and SEQ ID NO: 31.

[0420] The PCR reactions were then cooled to 37° C. and 20 units of therestriction endonuclease DpnI (New England Biolabs) was added to digestthe dam methylated pUC 19 template DNA and the reaction incubated at 37°C. for 90 minutes.

[0421] Following the DpnI treatment, the PCR products were purified fromunincorporated dNTPs, oligonucleotides, buffer, etc., using theStrataPrep PCR purification kit (Stratagene) using the manufacturersinstructions. Each purified PCR product was eluted from StrataPrepcolumns with dH₂O.

[0422] The various 2.6 kb pUC 19 PCR products were used in sticky RICEreactions with GFP PCR products from experiments 1A-1D (Examples 1A, 1B,1C and 1D) as described below:

Example 2A

[0423] Approximately 20 ng purified pUC 19 PCR product and 12 ng of a770 bp GFP PCR product were combined in a 10 ul reaction containing IXNEB ligase buffer, 0.2 mM (each) dGTP and dCTP, 0.8 Units T4 DNA pol(Novagen LIC qualified), 0.06 Units Gibco T4 DNA ligase and 0.6 Units T4polynucleotide kinase (Novagen). The reaction was incubated at roomtemperature for approximately 2.5 hours and then 1 ul was transformedinto DH5a chemically competent E. coli cells (Gibco). Approximately ⅕thof the transformed cells were then plated onto individual LB Agar platescontaining 100 ug/ml of Ampicillin and plates were incubated overnightat 37° C.

[0424] The following day, individual colonies were picked into 2 mlsamples of LB broth containing 100 ug/ml Ampicillin, and grown overnightin an incubator-shaker at 37° C. at approx 250-300 rpm. Plasmid DNA wasprepared from these overnight liquid cultures using the StrataPrepPlasmid Miniprep kit (Stratagene) according to the manufacturer'sinstructions.

[0425] To screen for the presence of a GFP sized DNA insert in plasmids,individual DNA samples of 2 ul were digested with the restrictionendonuclease AflIII (NEB) according to manufacturers suggestions. AflIIIwill cleave once in the pUC 19 backbone, and once in the GFP insert, torelease a DNA fragment of approximately 700 bp. AflIII digested DNAsamples were analyzed by electrophoresis through a 1% agarose gel in1×TAE buffer. The gel was then stained with Ethidium bromide stainingand photographed under UV light. The presence of a insert band of about700 bp indicated the presence of an insert in a plasmid.

[0426] The T4 DNA polymerase and dNTP treatment generated 5′ overhangson the two PCR products as described in the table below: pUC 19 PCRProduct 770 bp PCR Product PCR primers 351-352 349-350 used ds PCR prod5′tta ggt--------cc aat 5′aat ggc-----------acc tta aat cca-------gg tta  tta ccg-----------tgg aat Post T4 pol treat 5′tta ggt--------cc 5′aatggc-----------acc with dGTP/dCTP       cca--------gg tta      ccg-----------tgg aat

Example 2B

[0427] The sticky RICE reaction of Ex 2B was set up using substantiallythe same procedures of 2A except that 0.2 mM (each) dATP and dTTP wereused in place of 0.2 mM dGTP and dCTP, and PCR products of oligos (SEQID NO: 22)/(SEQ ID NO: 23) and (SEQ ID NO: 20)/(SEQ ID NO: 21) wereused.

[0428] The T4 DNA polymerase and dNTP treatment generated 5′ overhangson the two PCR products as described in the table below: pUC 19 PCRproduct 770 bp PCR Product PCR primers 355-356 353-354 used ds PCR prod5′ccg ttt---------taa ggc 5′ggc atg---------taa ccg   ggc aaa--------attccg   ccg tac---------att ggc Post T4 pol treat 5′ccg ttt---------taa5′ggc atg---------taa with dATP/dTTP      ∩aaa--------att ccg      tac--------att gg

[0429] The 5′ overhangs in bold are complementary to each other. The 5′overhangs underlined are complementary to each other.

Example 2C

[0430] The sticky RICE reaction of Ex 2C was set up using substantiallythe same procedures of 2A except that the PCR products of (SEQ ID NO:26)/(SEQ ID NO: 27) and (SEQ ID NO: 24)/(SEQ ID NO: 25) were used.

[0431] The T4 DNA polymerase and dNTP treatment generated 5′ overhangson the two PCR products as described in the table below: !pUC 19 PCRProduct? 770 bp PCR Product PCR primers 359-360 357-358 used ds PCR prod5′taa cct----------gaa aat 5′aaa atg g--------acc taa attgga----------ctt tta   ttt tac c-------tgg att Post T4 pol treat5′taa cct----------g 5′aaa atg g-------acc with dGTP/dCTP      gga----------ctt tta         c c-------tgg att

[0432] The 5′ overhangs in bold will be complementary to each other. The5′ overhangs underlined will be complementary to each other.

Example 2D

[0433] The sticky RICE reaction of Ex 2D was set up using substantiallythe same procedures of 2B except that PCR products of oligos (SEQ ID NO:30)/(SEQ ID NO: 31) and (SEQ ID NO: 28)/(SEQ ID NO: 29) were used.

[0434] The T4 DNA polymerase and dNTP treatment generated 5′ overhangson the two PCR products as described in the table below: !pUC 19 PCRproduct? 770 bp PCR Product PCR primers used 363-364 361-362 ds PCR prod5′ggc ttt----------aa cc 5′cc atg---------taa ggc   ccg aaa--------tt gg  gg tac---------att ccg Post T4 pol treat 5′ggc ttt----------aa 5′ccatg---------taa with dATP/dTTP       aaa---------tt gg     tac---------att ccg

[0435] The 5′ overhangs in bold are complementary to each other. The 5′overhangs underlined are complementary to each other.

[0436] Results of Examples 2A-2D: Rxn # colonies/plate % colonies withinserts 2A 6  2/8 (25%) 2B ca. 250 23/24 (96%) 2C >700 23/32 (72%)2D >700 21/32 (66%)

[0437]FIG. 3 is a photograph of a gel of the experimental results ofExample 2 (Sticky RICE cloning of inserts into pUC using T4 DNA ligase).Plasmids from the cloning reactions described in examples 2A-2D weredigested with AflIII to screen for the presence of a GFP insert.Plasmids with the GFP PCR product insert are expected to release a DNAfragment of approx. 700 bp after digestion with AflIII. Lanes of gel arenumbered from left to right. The far right and left lanes of both topand bottom half of gel contain 1 Kb DNA ladders from New EnglandBiolabs. The bottom half of the gel contains 8 isolates of clones fromexperiment 2A (lanes 2, 4, 6, 8, 10, 12, 14 and 16). Isolates ofexperiment 2B cloning are in the bottom of the gel, odd numbered lanes3-17, and lanes 18-33 (24 isolates total). Isolates of experiment 2C arein lanes 34-49 in the bottom of the gel, and lanes 2-17 in the top ofthe gel (32 isolates total). Isolates of experiment 2D are in lanes18-49 in the top of the gel (32 isolates total). The approx 700 bp bandis the lower of the two bands in lane 3 in the bottom of gel.

[0438] Experiment 3

[0439] Sticky RICE with E. coli DNA Ligase

[0440] Rxns 3A-3D were performed as described for 2A-2D, respectively,with the following modifications:

[0441] 1. The reactions were performed in IX E. coli DNA ligase buffer(New England Biolabs) supplemented with rATP to a final concentration of1 mM.

[0442] 2. Each 10 ul sticky RICE reaction contained 0.7 Units T4 DNA pol(Novagen LIC qualified), 6.6 Units E. coli DNA ligase (NEB) and 1.1Units T4 polynucleotide kinase (NEB).

[0443] 3. Reactions proceeded at room temperature overnight. Onemicroliter of each sticky RICE reaction (3A-3D) was transformed in toDH5a chemically competent E. coli cells (Gibco), according tomanufacturers instructions.

[0444] Approximately ½ of the entire sample of transformed cells wereplated on LB Agar plates containing 100 ug/ml Ampicillin and plates wereincubated overnight at 37° C.

[0445] The following day, individual colonies were picked into 2 mlsamples of LB broth containing 100 ug/ml Ampicillin, and grown overnightin an incubator-shaker at 37° C. at approx 250-300 rpm. Plasmid DNA wasprepared from these overnight liquid cultures using the StrataPrepPlasmid Miniprep kit (Stratagene) according to the manufacturer'sinstructions.

[0446] To screen for the presence of a GFP sized DNA insert in plasmids,individual DNA samples of 2 ul were digested with the restrictionendonuclease AflIII (NEB) according to manufacturers suggestions. AflIIIwill cleave once in the pUC 19 backbone, and once in the GFP insert, torelease a DNA fragment of approximately 700 bp. AflIII digested DNAsamples were analyzed by electrophoresis through a 1% agarose gel in1×TAE buffer. The gel was then stained with Ethidium bromide stainingand photographed under UV light. The presence of a insert band of about700 bp indicated the presence of an insert in a plasmid.

[0447] Results of Transformation Reaction. Reaction # colonies % cloneswith insert 3A 0 NA 3B >500 8/8 (100%) 3C 0 NA 3D >500 7/8 (88%) 

[0448]FIG. 4 is a photograph of a gel of the experimental results ofExample 3, (Sticky RICE cloning of inserts into pUC using E. coliligase). Lanes of gel are numbered left to right. Lanes 1 and 18 containa 1 Kb DNA ladder from New England Biolabs. Lanes 2-9 contain 8 isolatesof Exp 3B. Lanes 10-17 contain 8 isolates of Exp 3D. The approximately700 bp band released upon digestion with AflIII is the lower of the twobands in lane 4, for example. The AflIII restriction digest did not goto completion in all samples due to the large amount of DNA contained insome samples. This resulted in a partial DNA digest for many samples,though the unique 700 bp band can still be detected.

Example 4 Sticky RICE Cloning of PCR Fragments into a SapI Cut Vector

[0449] A tobacco mosaic virus based plant expression vector (Shivrasadet al 1999) was modified to contain 2 unique SapI restriction sites.

[0450] The typeII S restriction enzyme SapI, cleaves ds DNA to leave 3nt 5′ overhangs. A TMV based cDNA clone in a plasmid was generated withtwo SapI sites, such that SapI digested plasmid would be compatible witha sticky RICE cloning strategy of PCR products. This was accomplished asfollows:

[0451] Mutation of the SapI Site in the pUC DNA Backbone of a p30BGFPc3Vector (pCLONE5).

[0452] Since the desired plasmid will only have SapI sites in the TMVcDNA insert, the SapI site, which exists in the pUC plasmid backbone,must first be mutated. This was accomplished by using the PCR to amplifya portion of pCLONE5 DNA with oligos SEQ ID NO: 15 and 30B7093F,spanning from near the 3′ end of the virus cDNA insert, to justdownstream of the SapI site in the pUC backbone. The resulting PCRproduct was digested with the restriction enzymes KpnI and EarI,electrophoresed thru an agarose gel, and a ds DNA fragment ofapproximately 300 bp was isolated from the gel. This DNA fragment wasthen ligated to the approximately 10 Kb DNA fragment of a pCLONE5digested with SapI and KpnI. The resulting plasmid was named pC5DSapI.

[0453] pC5DSapI was digested with NcoI and PmlI (which cleave at nts5459 and 6536, respectively, in pC5DSapI). The resulting 9.3 kb fragmentwas gel isolated.

[0454] Using pCLONE5 template DNA, a DNA fragment of approximately 700bp was amplified using oligos SEQ ID NO: 34 and 30B5123F. Oligo SEQ IDNO: 34 will generate a SapI site fused to TMV cDNA vector sequences.

[0455] A cDNA insert of human thymosin cDNA was amplified and clonedinto pcDNA3.l V5 His topo cloning vector (Invitrogen). The thymosininsert and V5 His6 sequence was PCR amplified from this plasmid witholigos SEQ ID NO: 32 and a thymosin specific (forward) primer containinga PacI site near its 5′ end. This PCR product was digested with PacI andSalI and ligated into PacI-XhoI digested pCLONE5, in order to insert theV5 epitope and His6 coding sequence into the TMV cDNA. From thisplasmid, the V5 His6 sequence and downstream TMV vector sequence wasamplified by PCR with oligos SEQ ID NO: 35 and 30B6543R (a fragment ofabout 200 bp). Oligo SEQ ID NO: 35 will generate a SapI site justupstream of the V5 epitope coding sequence.

[0456] These two PCR fragments were joined together in a sticky RICEreaction by combining approximately equamolar amounts of PCR productswith T4 DNA polymerase and dGTP/dCTP blocking nucleotides, T4polynucleotide kinase, and T4 ligase in 1×NEB ligase buffer, underconditions similar to those described in Example 1.

[0457] After the Sticky RICE reaction, the reaction was extracted withphenol and chloroform and the DNA precipitated with ammonium acetate andethanol using standard conditions. The precipitated DNA was washed with70% EtOH, briefly dried and ultimately resuspended in dH₂O. This DNA wasthen digested with the restriction endonucleases NcoI and PmlI. Thedigested DNA was electrophoresed through an agarose gel and the approx570 bp fragment gel isolated. This approx. 570 bp fragment was thenligated into the approximately 10 Kb fragment of NcoI-PmlI digestedpC5DSapI. This generated the plasmid pLSB 1176 (see FIG. 13), which hasthe following (relevant) polylinker sequence:                                                        StsI           BstY I                                      Fok I     DraI  Bgl II                                      BstF5 I    |      |                                           |TCGTTTTAAATAgatcttacaGTATCACTACTCCatctcagttcgtgttcttgtcaggatAGCAAAATTTATctagaatgtCATAGTGATGAGGtagagtcaagcacaagaacagtccta    |    • |       •         •         •         •      |  •    5705   5712                                       5757 5760           5712                                       5757                                                      5757   SapI                               Mbo II                     EcoR V   TsPRI   Mbo II       Nhe I                 Ear I                  SfcI      Msl I   Ear I        AceII      BceF I    SapI                   Pst I     BstX I  |            |          |         |||                     |    |    ||  |gagaagagcTTTTTTGCTAGCGCGGAGCCGTTTTTTgctcttcaaaaccccaagacaattctgcagatatccagCACAGTctcttctcgAAAAAACGATCGCGCCTCGGCAAAAAAcgagaagttttggggttctgttaagacgtctataggtcGTGTCA  |      •     |   •      |  •      |||•         •         •|    |   •||  |    •5763         5776       5787      5797                    5821      5831     5840

[0458] Note the position of the 2 SapI sites (at approx nt 5763 and5797). The SapI site at 5763 cuts to its left, leaving an TAC5′ overhangon the bottom strand and the SapI site at 5797 cuts to its right,leaving a 5′ AAA overhang on the top strand.

[0459] For pLSB 1176, the following Oligos were used: SEQ ID NO: 15gactcttcaa gcgcaagagc gcccaatacg ca SEQ ID NO: 32 CggCTggTCg ACgCGggTTTA SEQ ID NO: 33 AACTCAATgg TgATg SEQ ID NO: 34 AAAAAAgCTC TTCTCATCCTgACAAgAACA CgAACTgAgA T SEQ ID NO: 35 TTTTTTgCTC TTCAAAACCC CAAgACAATTCTgCAgATAT CCAg SEQ ID NO: 36 TTTTTTgCTA gCgCggAgCC gTTTTTTgCTCTTCAAAACC CCAAgACA SEQ ID NO: 37 (30B 5123F) TgTTTAgCCg gTTTggTCgT SEQID NO: 38 (30B 7093F) TTgATCCgTT gATCACggCg T SEQ ID NO: 39 (30B 6543R)CACTATgCgT TATCgTACgC A

[0460] After digestion with SapI, the vector pLSB 1176 waselectrophoresed thru a 1% agarose in 1×TAE gel and isolated from thegel.

[0461] An insert was prepared for this vector by PCR of the GFPc3 genefrom pCLONE5 with the oligos: SEQ ID NO: 46 ATg CCC gCT AgC AAA ggA gAAgAA CTT TTC and SEQ ID NO: 47 TTT CCC ITT gTA gAg CTC ATC CAT gCC ATg

[0462] (SEQ ID NO: 46 is the Forward direction oligo for GFP and SEQ IDNO: 47 is the Reverse direction oligo for GFP) which would generate aPCR product of about 770 bp which, when treated with dGTP would givesticky ends compatible with the approximately 10 kb SapI digested pLSB1176 vector fragment (see table below). Insert DNA ends (SEQ ID NO: 40)SapI cut Vector DNA ends+HZ,1 45 Treat with T4 atg ccc GCT AGC--- tacaaa ggg aaa --cagg    aaa ccc--- DNA pol and tac ggg cga tcg-- atg tttccc ttt --gtcc tac     ggg--- dGTP post T4+dGTP atg ccc GCT AGC--- tacaaa ggg --cagg    aaa ccc--- treat     ggg cga tcg-- atg ttt ccc ttt--gtcc tac     ggg--+TZ,1 45

[0463] Note that in FIG. 13 the sticky ends of the SapI cut vector areunchanged by the T4+dGTP treatement. 24 ng of SapI cut pLSB 1176 vectorand 4 ng of PCR product were combined in a 10 ul rxn containing 0.2 mMdGTP in 1×NEB ligase buffer and 1.25 Units Novagen LIC qualified T4 DNApol. Reaction was incubated at 37° C. for about 30-40 min, and 0.5 Unitsof Gibco DNA ligase added to the reaction. The reaction was then mixedby pipetting and incubated at 16° C. overnight. One microliter of theovernight ligation mix was transformed into DH5a chemically competent E.coli cells (Gibco). After transformation the cells were plated on LBagar plates containing 100 ug/ml ampicillin. Plates were incubatedovernight at 37° C. The next day 12 colonies were picked from the platesand used to inoculate 2 ml samples of LB broth with 100 ug/mlampicillin. DNA was prepared from liquid cultures using the strataprepplasmid DNA purification system (Stratagene). DNA samples were screenedfor the presence of the GFP based PCR insert by digestion with therestriction endonuclease HindIII followed by agarose gel electrophoresisof the digested DNAs. Of 12 plasmids screened in this manner, all 12 hadinserts.

[0464]FIG. 5 is a photograph of a gel of the experimental results forExample 4 (Sticky RICE cloning of GFP PCR product into SapI digestedvector DNA—pLSB 1176). The lanes of gel are numbered from left to right.Lane 1 contains a 1 Kb DNA ladder from New England Biolabs. Lane 2contains HindIII digested pCLONE 5 control DNA (which already containsthe GFP insert). Clones of interest from the experiment will generatethe same HindIII restriction enzyme digestion pattern as the pCLONE 5control DNA. Lanes 3-14 contain isolates 1-12 of Experiment 4. Note allshow HindIII restriction enzyme digestion patterns equivalent to thecontrol.

Example 5 The effect of Relative Polymerase, Kinase and LigaseConcentrations on Sticky RICE Reactions

[0465] Experiments were conducted to examine the effect of relativepolymerase and kinase and ligase concentrations on the efficiency of theSticky RICE reaction. Various concentrations of kinase and polymerasewere assembled, keeping the T4 DNA ligase (Gibco/BRL) concentrationconstant at 0.25 units per reaction. Concentrations of T4 DNA polymerase(Novagen LIC qualified) from 2.5 U to 0 U were tested. T4 DNA kinase(New England Biolabs) concentrations between 2.5 and 0 U were alsotested. Each reaction consisted of 7.8 ng of a 225 bp PCR product, 25 ngof a 725 bp PCR product, 1 ul 10×ligase buffer (New England Biolabs), 1ul 2 mM dATP/dTTP stock solution in a final volume of 12.4 ul. Sourcesof enzymes were as follows: T4 DNA polymerase (Novagen, LIC qualified),T4 polynucleotide kinase (New England Biolabs), T4 DNA ligase(Gibco/BRL).

[0466] Two different temperatures were tested in this Sticky RICEexperiment. Reactions were either incubated at 37° C. for 10 minutesfollowed by 2 hours at room temp, or were treated only at roomtemperature for 2 hours. The Sticky RICE reactions were terminated byincubation at 75° C. for 10 minutes. Reactions were then electrophoresedon a 1.5% agarose gel (in 1×TAE buffer, Sambrook et al Molecular cloningmanual). After electrophoresis DNA was visualized by staining the gelwith ethidium bromide (EtBr) and photographed under long wave UV light,as per standard conditions (Sambrook et al.). To estimate the efficiencyof the Sticky RICE reaction the staining intensity of the approx 950 bpband (formed by the joining of the 225 and 725 bp DNA fragments, forexample the “top” band in Lane 10 of FIG. 6) relative to the stainingintensity of the 725 pb product was compared.

[0467] The 225 and 725 bp DNA fragments used in this Sticky RICEexperiment were obtained by amplifying portions of the plasmid pUC 19(using Pfu DNA polymerase from Stratagene Corp. and standard PCRreaction conditions, as suggested by the manufacturer) with thefollowing primers:

[0468] PCR Primers Used: SEQ ID NO: 15 5′ gactcttcaa gcgcaagagcgcccaatacg ca 3′ SEQ ID NO: 42 5′ ggcttagctg tttcctgtgt gaaattgtt 3′ SEQID NO: 43 5′ gccatggcta gcaaaggaga agaa c 3′ SEQ ID NO: 21 5′ cggttatttgtagagctcat ccatgcca 3′

[0469] The sequences of the 225 and 725 bp DNAs is presented below (225Seq and 775 Seq) 225 Seq: SEQ ID NO: 44 GACTCTTCA AGCGCAAGAGCGCCCAATACGCAA ACCGCCTCTCCC CGCGCGTTCGCC GATTCATTAATG CAGCTG GCACGACAGGTTTCCCGACTG GAAAGCGGGCAG TGAGCGCAACGC AATTAATGTGAG TTAGCTCACTCA TTAGGCACCCCAGGC TTTACACTTTAT GCTTCCGGCTCG TATGTTGTGTGG AATTGTGAGCGGATAACAATTTCA CACAGG AAACAGCTA AGCC 725 Seq: SEQ ID NO: 45 GCCATGAGTAAAGGAGAAGAA CTTTTCACTGGA GTTGTCCCAATT CTTGTTGAATTA GATGGTGATGTT AATGGGCACAAATTT TCTGTCAGTGGA GAGGGTGAAGGT GATGCAACATAC GGAAAACTTACCCTTAAATTTATT TGCACT ACTGGAAAA CTACCTGTTCCA TGGCCAACACTT GTCACTACTTTCTCTTATGGTGTT CAATGCTTTTCA AGATAC CCAGATCAT ATGAAACGGCAT GACTTTTTCAAGAGTGCCATGCCC GAAGGTTATGTA CAGGAAAGAACT ATATTT TTCAAAGAT GACGGGAACTACAAGACACGTGCT GAAGTCAAGTTT GAAGGTGATACC CTTGTTAATAGA ATCGAG TTAAAAGGTATTGATTTTAAA GAAGATGGAAAC ATTCTTGGACAC AAATTGGAATAC AACTATAACTCA CACAATGTATACATC ATGGCAGACAAA CAAAAGAATGGA ATCAAAGTTAAC TTCAAAATTAGACACAACATTGAA GATGGA AGCGTTCAA CTAGCAGACCAT TATCAACAAAAT ACTCCAATTGGCGATGGCCCTGTC CTTTTACCAGAC AACCAT TACCTGTCC ACACAATCTGCC CTTTCGAAAGATCCCAACGAAAAG AGAGACCACATG GTCCTTCTTGAG TTTGTA ACAGCTGCT GGGATTACACATGGCATGGATGAA CTATACAAATGA CCG

[0470] During the Sticky RICE reaction the 3′ ends of the PCR productswill be removed by the 3′ to 5′ exonuclease activity of the DNApolymerase, until the appropriate template nucleotide is reached. Inthis example the DNA is treated with T4 DNA polymerase in the presenceof dATP and dTTP so that 5′ overhangs consist of only of G and Cresidues as described below: 225 bp PCR product 726 bp PCR product frompUC19 from p30BGFPc3 PCR primers used: 308-397 398-354 ds PCR product:5′gac tct ----- taa gcc 5′gcc atg ----- taa ccg    ctg aga ----- att cgg   cgg tac ----- att ggc Post T4 pol treat 5′gac tct ----- taa 5′gcc atg----- taa with dATP/dTTP     tg aga -----att cgg       tac ----- att ggc

[0471] The amounts of polymerase, kinase and ligase in each reaction,and the gel loading is presented in Table 1. The gel image is shown inFIG. 6, below.

[0472] Note that not all combinations of polymerase, kinase and ligaseresulted detectable amounts of recombinant DNA joining in thisexperiment. The experimental results demonstrate that “too much” or “toolittle” kinase or polymerase can result in inefficient DNA joiningreactions. For example in Lane 1 a reaction with 2.5 U Pol, 2.5 U kinaseand 0.25 U ligase did not result in any detecable DNA joining, but thereaction in Lane 5 which had 1.5 U Pol, 2.5 Kinase and 0.25 U ligase didresult in detectable levels of DNA joining. Similarly the reaction inLane 13 (0.1 U Pol, 2.5 U kinase and 0.25 U ligase) did not produce anydetectable DNA joining, but the reaction in lane 63 (0.1 U Pol, 0.1 Ukinase and 0.25 U ligase) did generate detectable levels of DNA joining.These results demonstrate that the relative levels of these threeenzymatic activities dramatically effects the Sticky RICE reaction andthat not all enzyme ratios lead to efficient joining of DNAs in vitro.TABLE 1 Description of loading of gel shown in FIG. 6: Bottom Row, Leftto Right. Middle Row, Left to Right Top Row, Left to Right Lane Pol (U)Kinase (U) Ligase (U) Lane Pol (U) Kinase (U) Ligase (U) Lane Pol (U)Kinase (U) Ligase (U) 1 2.5 2.5 0.25 U 51 2.5 0.1 0.25 U 101 2.5 0.50.25 U 2 2.5 2 0.25 U 52 2.5 0 0.25 U 102 2.5 0.25 0.25 U 3 2 2.5 0.25 U53 2 0.1 0.25 U 103 2 0.5 0.25 U 4 2 2 0.25 U 54 2 0 0.25 U 104 2 0.250.25 U 5 1.5 2.5 0.25 U 55 1.5 0.1 0.25 U 105 1.5 0.5 0.25 U 6 1.5 20.25 U 56 1.5 0 0.25 U 106 1.5 0.25 0.25 U 7 1 2.5 0.25 U 57 1 0.1 0.25U 107 1 0.5 0.25 U 8 1 2 0.25 U 58 1 0 0.25 U 108 1 0.25 0.25 U 9 0.52.5 0.25 U 59 0.5 0.1 0.25 U 109 0.5 0.5 0.25 U 10 0.5 2 0.25 U 60 0.5 00.25 U 110 0.5 0.25 0.25 U 11 0.25 2.5 0.25 U 61 0.25 0.1 0.25 U 1110.25 0.5 0.25 U 12 0.25 2 0.25 U 62 0.25 0 0.25 U 112 0.25 0.25 0.25 U13 0.1 2.5 0.25 U 63 0.1 0.1 0.25 U 113 0.1 0.5 0.25 U 14 0.1 2 0.25 U64 0.1 0 0.25 U 114 0.1 0.25 0.25 U 15 0 2.5 0.25 U 65 0 0.1 0.25 U 1150 0.5 0.25 U 16 0 2 0.25 U 66 0 0 0.25 U 116 0 0.25 0.25 U 17 100 bpladder 67 100 bp ladder 117 100 bp ladder (Promega) 18 2.5 1.5 0.25 U 682.5 2.5 0.25 U 118 2.5 0.1 0.25 U 19 2.5 1 0.25 U 69 2.5 2 0.25 U 1192.5 0 0.25 U 20 2 1.5 0.25 U 70 2 2.5 0.25 U 120 2 0.1 0.25 U 21 2 10.25 U 71 2 2 0.25 U 121 2 0 0.25 U 22 1.5 1.5 0.25 U 72 1.5 2.5 0.25 U122 1.5 0.1 0.25 U 23 1.5 1 0.25 U 73 1.5 2 0.25 U 123 1.5 0 0.25 U 24 11.5 0.25 U 74 1 2.5 0.25 U 124 1 0.1 0.25 U 25 1 1 0.25 U 75 1 2 0.25 U125 1 0 0.25 U 26 0.5 1.5 0.25 U 76 0.5 2.5 0.25 U 126 0.5 0.1 0.25 U 270.5 1 0.25 U 77 0.5 2 0.25 U 127 0.5 0 0.25 U 28 0.25 1.5 0.25 U 78 0.252.5 0.25 U 128 0.25 0.1 0.25 U 29 0.25 1 0.25 U 79 0.25 2 0.25 U 1290.25 0 0.25 U 30 0.1 1.5 0.25 U 80 0.1 2.5 0.25 U 130 0.1 0.1 0.25 U 310.1 1 0.25 U 81 0.1 2 0.25 U 131 0.1 0 0.25 U 32 0 1.5 0.25 U 82 0 2.50.25 U 132 0 0.1 0.25 U 33 0 1 0.25 U 83 0 2 0.25 U 133 0 0 0.25 U 34100 bp ladder(Promega) 84 100 bp ladder(Promega) 134 100 bp ladder(Promega) 35 2.5 0.5 0.25 U 85 2.5 1.5 0.25 U 36 2.5 0.25 0.25 U 86 2.51 0.25 U 37 2 0.5 0.25 U 87 2 1.5 0.25 U 38 2 0.25 0.25 U 88 2 1 0.25 U39 1.5 0.5 0.25 U 89 1.5 1.5 0.25 U 40 1.5 0.25 0.25 U 90 1.5 1 0.25 U41 1 0.5 0.25 U 91 1 1.5 0.25 U 42 1 0.25 0.25 U 92 1 1 0.25 U 43 0.50.5 0.25 U 93 0.5 1.5 0.25 U 44 0.5 0.25 0.25 U 94 0.5 1 0.25 U 45 0.250.5 0.25 U 95 0.25 1.5 0.25 U 46 0.25 0.25 0.25 U 96 0.25 1 0.25 U 470.1 0.5 0.25 U 97 0.1 1.5 0.25 U 48 0.1 0.25 0.25 U 98 0.1 1 0.25 U 49 00.5 0.25 U 99 0 1.5 0.25 U 50 0 0.25 0.25 U 100 0 1 0.25 U

[0473] As can be seen from the data in FIG. 6, the Sticky RICE reactionefficiently joined the two DNA molecules over a wide range ofpolymerase, kinase and ligase levels. The most efficient reactions arein bold in the table above. Also the Sticky RICE reaction works eitherat a single temp (room temperature only) or when treated first at 37Cand then later shifted to room temperature.

Example 6 Effects of Temperature and Enzyme Levels on the Sticky RICEReaction Efficiency

[0474] Sticky RICE reactions were assembled as follows: The final volumeof each reaction was 12.4 ul. Each reaction contained 1 ul 10×NEB ligasebuffer, 25 ng of the 775 bp fragments described in Example 5 and 8 ng ofthe 225 bp fragment described in Example 5, as well as 1 ul 2 mMdTTP/dATP. Various amounts of polymerase (T4 DNA polymerase, Novagen,LIC qualified), ligase (Gibco) and kinase (NEB T4 polynucleotide kinase)were added to various reactions and the final volume brought to 12.4 ulwith dH₂O, as needed. TABLE 2 Reaction Conditions For Example 6 Rxn #:Pol (U) Kinase (U) Ligase 37 C. RT 1 1 unit 2 Units 0 10 min 60 min 2 12 0.1 10 min 60 min 3 1 2 0.25 10 min 60 min 4 1 2 0.5 10 min 60 min 5 12 0.75 10 min 60 min 6 1 2 1 10 min 60 min 7 1 2 2 10 min 60 min 8 1 20.25 10 min 60 min 9 0.25 0.5 0 10 min 60 min 10 0.25 0.5 0.1 10 min 60min 11 0.25 0.5 0.25 10 min 60 min 12 0.25 0.5 0.5 10 min 60 min 13 0.250.5 0.75 10 min 60 min 14 0.25 0.5 1 10 min 60 min 15 0.25 0.5 2 10 min60 min 16 0.25 0.5 0.75 10 min 60 min

[0475] All three enzyme activities were added to all reactions, exceptfor the control reactions (1 and 9), which had no ligase added.Reactions were incubated at 37C for 10 minutes, then left at roomtemperature for 1 hour with the following exceptions: For reactions 8and 16 only the polymerase and kinase activities were added, thereaction incubated at 37C for 10 minutes, then incubated at 75C for 10minutes to inactivate kinase and polymerase. Reactions 8 and 16 werethen cooled to room temp. and ligase added at the levels describedabove. Finally the reactions (8 and 16) were incubated at room temp for1 hour after the addition of ligase. All reactions were incubated at 75C for 10 minutes prior to being loaded onto a 1.5% agarose gel in 1×TAE.DNA bands were visualized by staining gel with EtBr and UV as describedfor Example 1 and is shown in FIG. 7, below. Note that the presence andintensity of the 1 Kb band demonstrates the efficiency of the stickyRICE reaction. The Sticky RICE reaction can be performed by treating theDNAs with kinase and polymerase and then inactivating the polymerase andkinase activities before adding the ligase (reactions 8 and 16).

[0476] In FIG. 7, the lanes are numbered left to right. Lane 1: Promega100 bp ladder. Lanes 2-17, reactions 1-16, respectively. Lane 18,Promega 100 bp ladder.

Example 7 Joining of PCR Products: Sticky RICE Cloning System

[0477] Directional Cloning System

[0478] Directional joining of PCR products using novel sticky RICEtechnology allows fast and efficient construction of recombinant DNAsfrom PCR products generated with proofreading or non-proofreadingpolymerases.

[0479] Features and Benefits

[0480] Join PCR products in less than 1 hour

[0481] Requires less primer design than sequence overlap extension (SOE)

[0482] High specificity directional joining of PCR products

[0483] Single temperature reaction

[0484] No restriction enzymes required

[0485] Principle

[0486] Sticky RICE, like the PCR-based technique of sequence overlapextension (SOE) can be used to directionally join double stranded DNAmolecules without the use of restriction enzymes.

[0487] Using the Sticky RICE enzyme mixture, sticky ends are generated,annealed and DNAs joined in a single temperature reaction in less timethan an SOE reaction. Since primer design is less complex than with SOEthe reaction is both easier and less expensive, and DNAs are joinedwithout the use of error prone DNA polymerases or thermocycling steps.

[0488] Specific Recombination in Less Than 1 Hour

[0489] Sticky RICE Recombination

[0490]FIG. 8A shows the results of directional joining of a 225 and 725bp PCR product sharing a 3 bp overlap. PCR products were combined withvarious amounts of sticky rice enzyme mixture and incubated at roomtemperature for 1 hour. Reactions were analyzed on a 1.5% agarose gel.Lanes 1-4, sticky RICE reactions with 0.5, 0.25, 0.1 or 0 ul of stickyRICE enzyme mix; M, 100 bp Marker. FIG. 8B depicted the basic steps ofSticky RICE Recombination in accordance with the present invention.

Example 8 Cloning of PCR Products: Sticky RICE Cloning System

[0491] Directional Cloning System

[0492] Directional ligation of PCR products using novel sticky RICEtechnology allows fast and efficient ligation of PCR products, generatedusing either proofreading or non-proofreading polymerases, intoplasmids. Features and benefit

[0493] No restriction enzymes needed

[0494] Directional cloning

[0495] Clone PCR products of proofreading or non-proofreadingpolymerases

[0496] Rapid ligation time

[0497] High cloning efficiency

[0498] Principle

[0499] Use the Sticky RICE technique to directionally ligate PCRproducts into a vector of choice without using restriction enzymes. PCRproducts amplified with any polymerase (proofreading ornon-proofreading) can be directly cloned.

[0500] Using the sticky RICE enzyme mixture sticky ends are generated,annealed and DNAs joined in a single temperature reaction in less timethan a typical restriction enzyme digestion. Recombinant plasmids aregenerated in a simple room temperature reaction.

[0501] High Efficiency Directional Cloning into a 10 kb Plasmid

[0502] Sticky RICE Cloning Kit Procedure

[0503]FIG. 9A depicts results of an experiment where a 0.8 kb PCRproduct was ligated into a 10 kb TMV expression vector plasmid usingSticky RICE. DNA samples from 12 isolates (lanes 1-12) were digestedwith HindIII and compared to HindIII digested positive control DNA (C).All 12 isolates gave the expected restriction enzyme digestion pattern.Lane M; MW marker. FIG. 9B shows the basic steps of a Sticky RICECloning Kit Procedure in accordance with the present invention.

[0504] In FIG. 10A, the basic steps of the Sticky RICE methodology arerepresented showing alternative ways to perform Sticky RICE and therebyjoining DNA fragments. Specifically, multiple double stranded DNAfragments A and B, shown in steps S1a and S1b, respectively, in FIG.10A, are treated with DNA polymerase and the appropriate blocking dNTPs(and optional DNA kinase activity) in separate reactions, as representedat steps S2a and S2b, respectively. In steps S2a and S2b, DNA kinaseactivity is optional and is therefore shown in parenthesis. Thereafter,there are two alternatives. First, following DNA polymerase treatment inthe presence of blocking dNTP(s), the fragments can be directlycombined, as indicated at step S3. Next, as shown at step S4, DNA ligaseactivity, DNA polymerase and blocking dNTP are added to the combinedfragments, resulting in the annealing and covalent joining of fragmentsA and B. The addition of kinase is also optional in step S4

[0505] Alternatively, after steps S2a and S2b, as shown in FIG. 10A, thefragments are inactivated at steps S5a and S5b by chemical means (cleanup of DNA using DNA purification kits such as Stratagene PCR clean upkit, or Qiaquick DNA clean up kit, etc.) or heat treatment (for example75° C. for 10 min) of the reactions, or the DNA can be separated fromthe enzymes (pol and kinase) by physical separation (for example use ofa CentriSep spin column, Princeton Separations, will removeunincorporated dNTPs, and proteins, from the reaction). Next, asindicated at step S6, the fragments are combined with ligase, DNApolymerase and blocking dNTP. Use if kinase in step S6 is optional.

[0506] To more clearly represent the two embodiments depicted in FIG.10A, FIGS 10B and 10C are provided with the two alternative embodimentsseparated. Specifically, in FIG. 10B, multiple double stranded DNAfragments A and B, shown in steps S1a and S1b, respectively in FIG. 10B,are treated with DNA polymerase and the appropriate blocking dNTPs (andoptional DNA kinase activity) in separate reactions, as represented atsteps S2a and S2b, respectively. In steps S2a and S2b, kinase activityis optional and is therefore shown in parenthesis. Thereafter, thefragments are directly combined, as indicated at step S3. Next, as shownat step S4, DNA ligase activity, DNA polymerase and blocking dNTPs areadded to the combined fragments, resulting in the annealing and covalentjoining of fragments A and B. The addition of kinase is also optional instep S4

[0507] As shown in FIG. 10C, after steps S2a and S2b, the enzymes areinactivated at steps S5a and S5b by chemical means (clean up of DNAusing DNA purification kits such as Stratagene PCR clean up kit, orQiaquick DNA clean up kit, etc.) or heat treatment (for example 75° C.for 10 min) of the reactions, or the DNA can be separated from theenzymes (pol and kinase) by physical separation (for example use of aCentriSep spin column, Princeton Separations, will remove unincorporateddNTPs, and proteins, from the reaction). Next, as indicated at step S6,after the separation of enzymes from the DNA fragments, or inactivationof the enzymes, the fragments are then combined and DNA ligase added tothe combined DNAs, allowing the DNA fragments to anneal and becomecovalently joined. Alternatively, DNA polymerase and additional blockingdNTPs, if needed, and kinase activities can be added in addition to DNAligase activity at this step.

[0508] In another embodiment of the present invention, shown in FIG.10D, the fragments A and B in steps S10a and S10b, respectively, arecombined in a vessel, as indicated at step S11, then DNA polymerase,blocking dNTPs, kinase if needed, and DNA ligase is added to thecombined DNAs allowing the DNA fragments to anneal and become covalentlyjoined, as indicated at step S12.

[0509]FIG. 14 shows generically a variety of alternative combination ofsteps for practicing the present invention that are expanded on andfurther explained with respect to FIGS. 15, 16A, 16B, 16C and 17.Specifically, FIG. 14 shows two alternative processing paths for theconstruction of linear expression elements, and more specifically geneexpression without cloning using the methods of the present invention,that are herein referred to as the Sticky RICE methodology. As shown inFIG. 14, a promoter element P, a gene of interest I and a terminatorelement T are PCR amplified. Thereafter, two differing processing pathsmay be followed, in accordance with different embodiments of the presentinvention.

[0510] For example, on the right hand side of FIG. 14, the promoter Pand a quantity of the gene of interest I may be joined in a 2-way StickyRICE reaction, and simultaneously another quantity of the gene ofinterest I may be joined with the terminator T. Thereafter, thereactions are combined and the DNA purified using a column basedpurification method. Next, the promoter P and terminator T are PCRamplified using specific primers resulting in a desired construct thatincludes the promoter P, the gene of interest I and the terminator T.Various combinations of treatments represented on the right hand side ofFIG. 14 are further embellished and described with respect to FIGS. 15,16A, 16B and 16C and Examples 9-33.

[0511] On the left hand side of FIG. 14, the promoter P, the gene ofinterest I and the terminator T are combined in a single 3 way reaction.The resulting DNA is then purified using column based purificationmethods and then PCR amplified with promoter and terminator specificprimers. Various combinations of treatments represented on the left handside of FIG. 14 are further embellished and explained with respect toFIG. 17 and Examples 34-41.

[0512] The plurality of embodiments presented below include variouscombinations of reactions where the individual reactions have alreadybeen described above. Therefore, Embodiments 9-41 are presented below ina concise tabular manner to more clearly demonstrate the variations inthe combinations of treatments used to practice the present invention,along with comments on the various combinations of treatments.

[0513]FIGS. 15, 16A, 16B, 16C and 17 show a variety of combination ofsteps that are used to practice the present invention. The basic stepsand embodiments represented in FIGS. 15, 16A, 16B and 16C are tallied inthe tables below: Step Treatment A1 Kinase treatment A2 Phosphatase/notreatment A3 Polymerase + blocking dNTPs and ligase (optional kinase) B1Phosphatase/no treatment B2 Kinase Treat B3 Polymerase + blocking dNTPsand ligase (optional kinase) C1 Phosphatase/no treatment C2Phosphatase/no treatment C3 Polymerase + blocking dNTPs and ligase andkinase D1 Kinase and Polymerase + blocking dNTPs treat D2 Kinase andPolymerase + blocking dNTPs treat D3 Ligase (Optional polymerase andblocking dNTPs, optional kinase) E1 Kinase and Polymerase + blockingdNTPs treat E2 Polymerase + blocking dNTPs treat E3 Ligase (optionalpolymerase and blocking dNTPs, optional kinase) F1 Polymerase + blockingdNTPs treat F2 Kinase and Polymerase + blocking dNTPs treat F3 Ligase(optional polymerase and blocking dNTPs, optional kinase) G1 Polymeraseand blocking dNTPs treatement G2 Polymerase and blocking dNTPstreatement G3 Kinase and ligase treatment (optional polymerase andblocking dNTPS H1 Kinase treatment H2 Kinase treatment H3 Polymerase andblocking dNTPs, ligase, (optional kinase)

[0514] Figure Embodiment Steps Treatment Of: 15 9 A₁, A₂ & A₃ P, I and P& I respectively 15 10 B₁, B₂ & B₃ P, I and P & I respectively 15 11 C₁,C₂ & C₃ P, I and P & I respectively 15 12 D₁, D₂ & D₃ P, I and P & Irespectively 15 13 E₁, E₂ & E₃ P, I and P & I respectively 15 14 F₁, F₂& F₃ P, I and P & I respectively 15 15 G₁, G₂ & G₃ P, I and P & Irespectively 15 16 H₁, H₂ & H₃ P, I and P & I respectively 16A 17 A₁, A₂& A₃ P, I and P & I respectively 16A 18 B₁, B₂ & B₃ P, I and P & Irespectively 16A 19 C₁, C₂ & C₃ P, I and P & I respectively 16A 20 D₁,D₂ & D₃ P, I and P & I respectively 16A 21 E₁, E₂ & E₃ P, I and P & Irespectively 16A 22 F₁, F₂ & F₃ P, I and P & I respectively 16A 23 G₁,G₂ & G₃ P, I and P & I respectively 16A 24 H₁, H₂ & H₃ P, I and P & Irespectively 16B 25 A₁, A₂ & A₃ I, T and I & T respectively 16B 26 B₁,B₂ & B₃ I, T and I & T respectively 16B 27 C₁, C₂ & C₃ I, T and I & Trespectively 16B 28 D₁, D₂ & D₃ I, T and I & T respectively 16B 29 E₁,E₂ & B₃ I, T and I & T respectively 16B 30 F₁, F₂ & F₃ I, T and I & Trespectively 16B 31 G₁, G₂ & G₃ I, T and I & T respectively 16B 32 H₁,H₂ & H₃ I, T and I & T respectively 16C 33 PCR P & I and I & T

[0515] Comments on Treatments:

[0516] Sticky RICE joining of DNA molecules is accomplished through theuse of multiple enzymatic activities, either in a concurrent orstep-wise fashion. Examples of how the individual or co-enzymatictreatments can be accomplished are described below. Permutations of thedescribed treatments can also be performed to accomplish the desiredtreatment outcome.

[0517] Phosphatase Treatment/No Treatment

[0518] If one wishes to remove 5′ phosphate groups from a DNA (as inFIG. 15A₂) this can be accomplished by incubating a DNA molecule in thepresence of shrimp alkaline phosphatase (Boehringer-mannheim) or Calfalkaline phosphatase (New England Biolabs) according to themanufacturers instructions (of buffer, time, temperature, DNAconcentration, etc) using either the buffer supplied by the manufactureror other suitable buffer/reaction conditions which allow the enzyme toeffectively remove 5′ phosphates from DNA.

[0519] If desired the phosphatase treatement can be terminated by hightemperature incubation of the reaction (for example shrimp alkalinephosphatase is inactivated by 15 min treatment at 65° C.), or purifyingthe DNA using a commercial DNA clean up kit according to themanufacturers instructions.

[0520] If the DNA does not have 5′ phosphate groups (because of aprevious treatment with phosphatase, or the DNA fragment was amplifiedusing PCR and primers without 5′ phosphate groups, for example), thephosphatase treatment is not necessary.

[0521] The phosphatase/No treatment applies to steps (A2, B1, C1, C2,AA1, AA2, AA3, AB1, AB3, AC2 in FIGS. 15-17)

[0522] Kinase Treatment:

[0523] If one wishes to add, or ensure that a DNA molecule has 5′phosphate groups, this can be accomplished by incubating a DNA moleculein the presence of rATP and a nucleotide kinasing enzyme such aspolynucleotide kinase which is available from a number of sources(inlcuding New England Biolabs, Promega, Invitrogen, etc.), according tothe manufacturers instructions of buffer, time, temperature, DNAconcentration, etc.

[0524] If desired the phosphatase treatement can be terminated by hightemperature incubation of the reaction (for example T4 polynucleotidekinase from New England Biolabs is inactivated by treatement at 65C for20 minutes), or by purifying the DNA using a commercial DNA clean up kitaccording to the manufacturers instructions.

[0525] The Kinase treatment step applies to steps (A1, B2, H1, H2, AB2,AC1, AC3, AH1, AH2, AH3 in FIGS. 15-17)

[0526] Polymerase Treatment with Blocking NTPs

[0527] If one wishes to generate 5′ overhangs on a DNA molecule, thiscan be accomplished by incubating a DNA molecule in the presence of aDNA polymerase activity with 3′ to 5′ exonuclease activity using themanufacturers instructions as a guideline. For example T4 DNA polymerasefrom New England Biolabs can function under a variety of temperature andbuffer conditions and the concentration of blocking dNTPs to be used aresuggested to be 100 mM.

[0528] If desired the polymerase+blocking dNTP reaction can beterminated by high temperature incubation of the reaction (for exampleT4 DNA polymerase from New England Biolabs is inactivated by treatmentat 75° C. for 10 minutes), or by purifying the DNA using a commercialDNA clean up kit according to the manufacturers instructions.

[0529] The polymerase with blocking dNTP(s) step applies to steps (E2,F1, G1, G2, AD2, AE1, AE2, AE3, AG1, AG3 in FIGS. 15-17).

[0530] Polymerase+Blocking dNTP(s) and Kinase Co-Treatment.

[0531] If one desires to ensure that the 5′ ends of a DNA moleculecontain 5′ phosphate groups and also to generate or maintain 5′overhangs on a DNA molecule during the same step a DNA molecule can beincubated in the presence of DNA polymerase (with 3′ to 5′ exonucleaseactivity and the appropriate blocking dNTPs) and a polynucleotide kinaseactivity in the presence of rATP (manufacturers of polynucleotide kinasegenerally suggest that the final rATP concentration by 1 mM) in a bufferin which both enzyme activities are active. For example both T4 DNApolymerase and T4 polynucleotide kinase have been demonstrated tofunction in T4 DNA ligase buffer (New England Biolabs) supplemented withthe appropriate blocking dNTPs. (FIG. 6).

[0532] If desired the polymerase+blocking dNTP and coupled kinasetreatement reaction can be terminated by high temperature incubation ofthe reaction (for example 75° C. for 20 minutes would inactivate both T4DNA polymerase and T4 polynucleotide kinase activities), or by purifyingthe DNA using a commercial DNA clean up kit according to themanufacturers instructions.

[0533] The polymerase+blocking dNTP(s) and kinase co-treatment appliesto steps (D1, D2, E1, F2, AD1, AD3, AF1, AF2, AF3, AG2 in FIGS. 15-17).

[0534] Polymerase+Blocking dNTP(s) and DNA Ligase Co-Treatment.

[0535] If one desires to generate or maintain 5′ overhangs on a DNAmolecule and also allow complementary 5′ overhangs to anneal and becomeligated in a single reaction, this can be accomplished by treatingmultiple DNA molecules in the presence of a DNA ligase activity and aDNA polymerase activity (with 3′ to 5′ exonuclease activity) in thepresence of the appropriate blocking dNTPs.

[0536] For example T4 DNA polymerase and T4 DNA ligase from New EnglandBiolabs are both active in 1×T4 DNA ligase buffer (New England Biolabs)supplemented to blocking dNTPs.

[0537] If desired the polymerase+blocking dNTP and coupled ligasetreatement reaction can be terminated by high temperature incubation ofthe reaction (for example 75° C. for 20 minutes would inactivate both T4DNA polymerase and T4 DNA ligase activities), or by purifying the DNAusing a commercial DNA clean up kit according to the manufacturersinstructions.

[0538] The polymerase+blocking dNTP(s) and DNA ligase co-treatment (withor without the optional components described) applies to steps (A3, B3,C3, H3, AA4, AB4, AC4, AH4) in FIGS. 15-17.

[0539] Kinase and Ligase Co-Treatment of DNAs.

[0540] If one desires to ensure that DNA molecules have 5′ phosphategroups and that DNA fragments can be ligated together in a single step,this can be accomplished by treating multiple DNA molecules in thepresence of polynucleotide kinase and DNA ligase activities undersuitable reaction conditions. For example T4 polynucleotide kinase andT4 DNA ligase from New England Biolabs are both functional in 1×T4 DNAligase buffer from New England Biolabs, at a variety of temperatures.

[0541] If desired the kinase and coupled ligase treatment reaction canbe terminated by high temperature incubation of the reaction (forexample 75° C. for 20 minutes would inactivate both T4 DNA polymeraseand T4 DNA ligase activities), or by purifying the DNA using acommercial DNA clean up kit according to the manufacturers instructions.

[0542] The kinase and ligase co-treatment applies to steps G3, AE4, inFIGS. 15-17. Ligase Treatment

[0543] If one wishes to covalently join DNA molecules together this canbe accomplished by treating multiple DNAs in the presence of a DNAligase activity under the appropriate conditions. See manufacturerssuggested reaction conditions of buffer, DNA concentration, reactiontemperature, etc. Optionally appropriate amounts of kinase and orpolymerase in the presence of blocking dNTPs can be also added to theligase treatment.

[0544] The ligase (with optional kinase and or optionalpolymerase+blocking dNTPs) treatment applies to steps D3, E3, F3, AD4,AF4, AG4) in FIGS. 15-17.

[0545] Polymerase+Blocking dNTPs, and Ligase and Kinse Co-Treatment:

[0546] If one wishes to maintain or generate 5′ single strandedoverhangs on multiple DNA molecules, generate 5′ phosphate groups on DNAmolecules, and allow multiple DNA molecules to be joined, this can beaccomplished by incubating multiple DNAs in the presence of polymeraseactivity (+the appropriate blocking dNTPs), DNA kinase activity and DNAligase activity in a single reaction, using the buffer and enzyme ratiosdescribed in FIG. 6, for example.

[0547] The Polymerase+blocking dNTPs, and ligase and Kinse co-treatmentstep applies to steps (C3 and AA4) in FIGS. 15-17.

[0548] As presented in FIG. 6, it is important to note that not allcombinations of polymerase, kinase and ligase activities can function togenerate recombinant DNA molecules. The ratio of the multiple enzymeactivities must be balanced to ensure that all enzyme activitiesfunction at a rate consistent with the desired output in terms ofquality and quantity of recombinant DNA produced in the desired timeframe. The in vitro DNA joining assay in FIG. 6 demonstrates that “toomuch” or “too little” of one or more enzyme activities can dramaticallyeffect the DNA joining reaction rate. Using the assay and conditionssimilar or identical to those described for FIG. 6 a researcher canreadily identify the enzyme mixture(s) which can accomplish the desiredoutput.

[0549] Multiple Applications for the Sticky RICE Workflow in FIG. 15.

[0550] Using the various combinations of work flow outlined in FIG. 15,sticky RICE can be used to generate recombinant DNAs for a variety ofapplications including, but not limited to, manual or automated cloningof DNAs into plasmids, production of recombinant RNAs for in vitro or invivo transcription and/or translation and production of double strandedRNA for RNAi applications.

[0551] Cloning Applications:

[0552] The work flow outlined in FIG. 15 can also be used for cloning aninsert DNA fragment (I) into a plasmid (P) DNA fragment. In thisscenario the desired outcome is a circular recombinant DNA moleculewhich can replicate in a cell such as bacterial, plant, animal, fungalor insect cells, for example. A circular molecule will result from thework flow outlined in FIG. 15, if both ends of the DNA fragment P becomeligated to opposite ends of fragment I. This can be readily accomplishedby appropriately designing the nucleotide sequence on the ends offragments P and I so that a circular molecule will result during stickyRICE joining of fragments P and I.

[0553] The work flow in FIG. 15 is designed to be modular in nature, toallow the user to treat fragments P and I independently, if desired.This also allows the user to control the treatments of fragments P and Iseparately, if desired by altering the amount of time, enzyme amounts,etc. in the separate treatments. Enzymatic treatments of the DNAs can bestopped by inactivation of enzymes (by heat treatment, for example) orby separation of the DNA from the enzymes (by purification of DNA byprecipitation, or use of commercial DNA “clean up kits” such as QiagenPCR clean up kits, Stratagene PCR clean up kits, etc.).

[0554] In an automated cloning system, for example, it would be possibleto pre-treat multiple aliquots (in a 96 well plate, for example) ofplasmid vector (fragment P) with a phosphatase enzyme (such as calfalkaline or shrimp alkaline phosphatase) to remove phosphates from the5′ ends of DNA P (FIG. 15, I1). After adequate phosphatase treatment thephosphatase enzyme can be inactivated by incubating the plate at anelevated temperature. For example shrimp alkaline phosphatase isinactivated by a heat treatment for 15 minutes at 65 C,Boehringer-mannheim. The present invention may be automated using, forinstance, a computer controlled liquid handler, such as that marketedand sold by TECAN, Zurich Switzerland.

[0555] In a separate plate, aliqouts of various insert DNAs (the Ifragments in FIG. 15 workflow) can be pre-treated with a kinase enzymefor, example (FIG. 15, I2). After adequate kinase treatment of a plateof I fragments, the kinase reaction can be terminated by heatinactivation. For example T4 polynucleotide kinase is inactivated by 20minute treatment at 65 C (New England Biolabs).

[0556] The pretreated P and I samples can then be combined (FIG. 1513)and treated with DNA ligase, DNA polymerase+the appropriate blockingdNTPs to allow for the joining of fragments P and I.

[0557] In a similar manner, each of the other work flows outlined inFIG. 15 can be readily adapted to an automated cloning system.

[0558] Using the guidelines described earlier in this patent, it ispossible to design plamsid vector DNAs (P fragments in FIG. 15) andinsert DNAs (I fragments in FIG. 15) which can be joined in either adirectional or a non-directional orientation via sticky RICE techniques.RNAi/dsRNA applications:

[0559] The work flows outlined in FIG. 15 can also be used to generatelinear recombinant DNAs which can be useful for generating RNAs.

[0560] For example, if one is interested in generating ds RNA molecules(for RNAi applications, for example) the work flow outlined in FIG. 15can be applied as follows. If fragment I is designed to have identical5′ single stranded overhangs on each end, and fragment P hascomplementary 5′ single stranded overhangs, then fragment P can bejoined to either or both ends of fragment I to generate the threedifferent linear recombinant DNA molecules represented at the bottom ofFIG. 15.

[0561] This can be of interest, in particular, if the researcher isinterested in generating double stranded RNA molecules in vitro or invivo. For example, if fragment P contains a functional promoter sequencethen transcription of the resulting population of recombinant DNAs withfunctional promoters attached to the “Left” end only and “Right” endonly of fragment I will generate RNA molecules of complementarysequence. These RNA molecules may hybridize and form ds RNA. Similarlytranscription of a recombinant DNA with functional promoters on bothends will also result in complementary RNA molecules, which mayhybridize to form ds RNA.

[0562] If the researcher is interested in generating RNAs which willform hairpins, then fragment I must have a nucleotide sequence whichupon transcription will generate an RNA molecule with selfcomplementarity to form a hairpin. One way in which this can beaccomplished is by synthesizing an oligonucleotide which is capable ofreadily forming a primer dimer. For example the oligo nucleotide of thesequence:

[0563] 5′ CT TAC gTA CTT gCA CCA TCC ATg gA (Seq ID No. 48)

[0564] has 8 nt of self complementarity on its 3′ end. Because of thistendency to dimerize at its 3′end (see below): 5′CT TAC gTA CTT gCA CCATCC ATg gA (Seq ID No.: 49)                        {overscore( AGG TAC CT ACc ACG TTC ATG CAT TC5′)} (Seq ID No.: 50)

[0565] when this oligo is allowed to anneal to itself (the estimated Tmof the 8 nts which are complementary would be about 24° C.) in thepresence of the appropriate buffer, dNTPs and DNA polymerase enzyme(such as T7-, T4-, or E. coli/Klenow DNA polymerase) a ds invertedrepeat DNA (of the following sequence) will be generated: 5′CT TAC gTACTT gCA CCA TCC ATg gA tgg tgc aag tac gta ag (Seq ID No.: 51)   ga atgcat gaa cgt ggt agg TAC CT ACc ACG TTC ATG CAT TC5′ (Seq ID No.: 52)

[0566] Note that the critical feature in this example is the selfcomplementarity at the 3′ end of the oligonucleotide and not theoligonucleotide sequence per se; the sequence of the oligonucleotide canbe changed. The generated inverted repeat DNA molecule, if transcribed,would generate a double stranded RNA molecule, which could be used forapplications such as RNAi for example. To join a DNA promoter elementvia sticky RICE to one or both ends of the inverted repeat DNA one maytreat the inverted repeat DNA sequence with polymerase with 3′ to 5′exonuclease activity in the presence of dATP and dTTP blockingnucleotides to generate single 5′ nt C overhangs on both ends of theinverted repeat DNA. This can then be joined to a DNA molecule (such asa promoter, for example) with a complementary 5′ G overhang. Thisjoining process can be accomplished using sticky RICE and any of thework flows outlined in FIG. 15.

[0567] Because the promoter element can go on either or both ends of theinverted repeat DNA sequence the possible DNA products could be: P---I    I---P P---I---P

[0568] as represented at the bottom of FIG. 15.

[0569] All of these recombinant DNAs (or the appropriate PCR productsthereof) can be transcribed (either in vitro and/or in vivo, dependingupon the functionality of the promoter in DNA fragment P) to generate ds(hairpin) RNA molecules useful in applications such as RNAi.

[0570] Applications for the Work Flow of FIGS. 16A-16C:

[0571] The work flows outlined in FIGS. 16A and B can be used toconstruct primarily a single recombinant DNA molecule. For example iffragments P and I (FIG. 16A) are designed (using the guidelinesdescribed earlier in this patent) for sticky RICE joining in adirectional orientation, the primary recombinant molecule produced wouldbe the linear recombinants DNA pictured at the bottom of FIG. 16A

[0572] If fragment P has promoter activity (either in vitro and/or invivo) the resulting linear recombinant (or the appropriate PCR productthereof) can be transcribed under the appropriate conditions to generatean RNA molecule.

[0573] The recombinant “P—I” molecule can be used for many applicationsby itself, including in vitro transcription and/or translationapplications for producing proteins in vitro or in vivo, for example.The recombinant “P—I” molecule can be used in applications directly orcan be amplified up using the polymerase chain reaction and suitableprimers. The amplified recombinant molecule can then be used inapplications as desired.

[0574] In a separate set of reactions, a second fragment “T” (see FIG.16B) can be designed to be joined to only the “right” end of the samefragment I as in FIG. 16A, to produce the linear recombinant moleculerepresented in the bottom of FIG. 16B.

[0575] If fragment T has promoter activity (either in vitro and/or invivo) the resulting linear recombinant (or the appropriate PCR productthereof) can be transcribed under the appropriate conditions to generatean RNA molecule.

[0576] When the transcripts from the recombinant DNA produced from thework flow in FIG. 16A are in the presence of transcripts from therecombinant DNA produced from the work flow in FIG. 16B, the twopopulations of RNA molecules may hybridize (because they arecomplementary in sequence) to generate a ds RNA molecule. This ds RNAgenerated can be useful for applications such as RNAi for example.

[0577] The product of FIG. 16A and FIG. 16B can be transcribed in thesame tube, vessel or cell, or in seperate tubes and then combined togenerate ds RNAs.

[0578] Similar to the description for FIG. 15, the work flows in FIGS.16A and 16B can also be automated. Fragments P and I and T, for examplecan be seperately treated in 96 well plates for example and thencombined as desired to generate the desired recombinant molecules.

[0579] Other applications of the workflows outlined in FIGS. 16A and 16Binclude the production of gene fusions by joining of multiple DNAfragments. For example a recombinant DNA product of two reading framesencoded by fragments P and I can be joined using the work flow oultinedin FIG. 16A or 16B.

[0580] For some applications it may be of interest to generate arecombinant DNA molecule of three or more DNAs joined in a directionalmanner. This can be accomplished using the work flows outlined in FIGS.16A-16C. For example the output from FIG. 16C is a recombinant DNA ofDNAs P, I and T, joined to generate a recombinant of the followingorientation “P-I-T” as represented in FIG. 16C. Applications of such arecombinant molecule include in vitro transcription, in vitrotranscription and translation and in vivo transcription/and ortranslation applications.

[0581] For example, if one desires to construct a linear recombinant DNAwhich can be transcribed in vitro or in vivo, it may be of interest toattach a promoter P fragment to one specific end of DNA fragment I and aDNA fragment T, which has transcription termination/polyadenylationfunctions, etc. to the other end of fragment I. This can be accomplishedin a step wise fashion following the work flows outlined in FIGS. 16A-C.To construct the 3-way recombinant DNA molecule described in FIG. 16C,the product of the work flow of FIG. 16A (P-I recombinant) and theproduct of the work flow from FIG. 16B (the I-T recombinant) can becombined in a single reaction vessel and subjected to polymerase chainreaction (PCR) conditions using primers that anneal specifically tofragments P and T, as represented by the arrows in FIG. 16C. During thepolymerase chain reaction the P-I-T recombinant DNA molecule will begenerated.

[0582] The P-I-T recombinant molecule produced can be used inapplications such as protein production, if fragment P has promoteractivity, and fragments I and or T contain an open reading frame. TheP-I-T recombinant DNA can be used to program in vitro transcription andor transcription/translation reactions to product recombinantprotein(s). Similarly the P-I-T recombinant molecule can be introducedinto living cells by microinjection, transfection, etc. to allow theP-I-T recombinant to be transcribed in vivo and the RNA potentiallytranslated to produce protein(s) in living cells.

[0583] In FIG. 17, various combinations of treatments are depicted inthe workflows. The table below sets forth the various steps and theportion of the sequence being treated. Table Of Various Steps Shown InFIG. 17 Step Treatment AA1 Phosphatase/no treatment AA2 Phosphatase/notreatment AA3 Phosphatase/no treatment AA4 Polymerase + blocking dNTPsand ligase and kinase treat AB1 Phosphatase/no treatment AB2 KinaseTreat AB3 Phosphatase/no treatment AB4 Polymerase + blocking dNTPs andligase (optional kinase) AC1 Kinase treat AC2 Phosphatase/no treatmentAC3 Kinase treat AC4 Polymerase + blocking dNTPs and ligase (optionalkinase) AD1 Kinase and Polymerase + blocking dNTPs treat AD2Polymerase + blocking dNTPs treat AD3 Kinase and Polymerase + blockingdNTPs treat AD4 Ligase (Optional polymerase and blocking dNTPs, optionalkinase) AE1 Polymerase + blocking dNTPs treat AE2 Polymerase + blockingdNTPs treat AE3 Polymerase + blocking dNTPs treat AE4 Ligase and Kinase(optional polymerase and blocking dNTPs) AF1 Kinase and Polymerase +blocking dNTPs treat AF2 Kinase and Polymerase + blocking dNTPs treatAF3 Kinase and Polymerase + blocking dNTPs treat AF4 Ligase (optionalkinase, optional polymerase and blocking dNTPs) AG1 Polymerase +blocking dNTPs treatement AG2 Kinase and Polymerase + blocking dNTPstreatement AG3 Polymerase + blocking dNTPs treatement AG4 Ligasetreatment (optional polymerase + blocking dNTPS, optional kinase) AH1Kinase treatment AH2 Kinase treatment AH3 Kinase treatment AH4Polymerase and blocking dNTPs, ligase, (optional kinase)

[0584] Figure Example Steps Treatment Of: 17 34 AA₁, AA₂, AA₃ & AA₄ P,I, T and P, I & T respectively 17 35 AB₁, AB₂, AB₃ & AB₄ P, I, T and P,I & T respectively 17 36 AC₁, AC₂, AC₃ & AC₄ P, I, T and P, I & Trespectively 17 37 AD₁, AD₂, AD₃ & AD₄ P, I, T and P, I & T respectively17 38 AE₁, AE₂, AE₃ & AE₄ P, I, T and P, I & T respectively 17 39 AF₁,AF₂, AF₃ & AF₄ P, I, T and P, I & T respectively 17 40 AG₁, AG₂, AG₃ &AG₄ P, I, T and P, I & T respectively 17 41 AH₁, AH₂, AH₃ & AH₄ P, I, Tand P, I & T

[0585] The various individual treatment steps outlined in workflows inFIG. 17 and referred to in the tables have all been described above. Toavoid duplicative text, comments will not be repeated.

[0586]FIG. 18 shows a computer and a TECAN fluid handler for effectingan automated process for practicing the present invention. Specifically,the computer is programmed to control fluid manipulating aspects of theTECAN in order to add the respective sequences, P, I and/or T along withappropriate reagents, enzymes, etc., for effecting the various methodsset forth in the drawings and the description above.

[0587] Various details of the present invention may be changed withoutdeparting from its spirit or its scope. Furthermore, the foregoingdescription of the embodiments according to the present invention areprovided for illustration only, and not for the purpose of limiting theinvention as defined by the appended claims and their equivalents.

1 52 1 10 DNA Artificial Sequence Misc. recombinant sequence 1ggttttttgg 10 2 10 DNA Artificial Sequence Misc. reombinant sequence 2ccaaaaaacc 10 3 28 DNA Artificial Sequence PCR primer 3 ggccttatggctagcaaagg agaagaac 28 4 25 DNA Artificial Sequence PCR Primer 4gcttgtagag ctcatccatg ccatg 25 5 12 DNA Artificial Sequence PCR Primer 5gccatgggca tt 12 6 32 DNA Artificial Sequence PCR Primer 6 gactcttcaagcgcaagagc gcccaatacg ca 32 7 29 DNA Artificial Sequence PCR Primer 7ggcttagctg tttcctgtgt gaaattgtt 29 8 238 DNA Artificial SequenceExperimental PCR Product 8 gactcttcaa gcgcaagagc gcccaatacg caaaccgcctctccccgcgc gttggccgat 60 tcattaatgc agctggcacg acaggtttcc cgactggaaagcgggcagtg agcgcaacgc 120 aattaatgtg agttagctca ctcattaggc accccaggctttacacttta tgcttccggc 180 tcgtatgttg tgtggaattg tgagcggata acaatttcacacaggaaaca gctaagcc 238 9 25 DNA Artificial Sequence PCR Primer 9gccatggcta gcaaaggaga agaac 25 10 28 DNA Artificial Sequence PCR Primer10 cggttatttg tagagctcat ccatgcca 28 11 726 DNA Artificial SequenceExperimental PCR Product 11 gccatggcta gcaaaggaga agaacttttc actggagttgtcccaattct tgttgaatta 60 gatggtgatg ttaatgggca caaattttct gtcagtggagagggtgaagg tgatgctaca 120 tacggaaagc ttacccttaa atttatttgc actactggaaaactacctgt tccatggcca 180 acacttgtca ctactttctc ttatggtgtt caatgcttttcccgttatcc ggatcatatg 240 aaacggcatg actttttcaa gagtgccatg cccgaaggttatgtacagga acgcactata 300 tctttcaaag atgacgggaa ctacaagacg cgtgctgaagtcaagtttga aggtgatacc 360 cttgttaatc gtatcgagtt aaaaggtatt gattttaaagaagatggaaa cattctcgga 420 cacaaactcg agtacaacta taactcacac aatgtatacatcacggcaga caaacaaaag 480 aatggaatca aagctaactt caaaattcgc cacaacattgaagatggatc cgttcaacta 540 gcagaccatt atcaacaaaa tactccaatt ggcgatggccctgtcctttt accagacaac 600 cattacctgt cgacacaatc tgccctttcg aaagatcccaacgaaaagcg tgaccacatg 660 ggccttcttg agtttgtaac tgctgctggg attacacatggcatggatga gctctacaaa 720 taaccg 726 12 28 DNA Artificial Sequence PCRPrimer 12 ccgttttaag ccagccccga ccacccgc 28 13 24 DNA ArtificialSequence PCR Primer 13 gatgagcgga tacatatttg aatg 24 14 302 DNAArtificial Sequence Experimental PCR Product 14 ccgttttaag ccagccccgacacccgccaa cacccgctga cgcgccctga cgggcttgtc 60 tgctcccggc atccgcttacagacaagctg tgaccgtctc cgggagctgc atgtgtcaga 120 ggttttcacc gtcatcaccgaaacgcgcga gacgaaaggg cctcgtgata cgcctatttt 180 tataggttaa tgtcatgataataatggttt cttagacgtc aggtggcact tttcggggaa 240 atgtgcgcgg aacccctatttgtttatttt tctaaataca ttcaaatatg tatccgctca 300 tc 302 15 32 DNAArtificial Sequence PCR Primer 15 gactcttcaa gcgcaagagc gcccaatacg ca 3216 23 DNA Artificial Sequence PCR Primer 16 aatggctagc aaaggagaag aac 2317 28 DNA Artificial Sequence PCR Primer 17 taaggttatt tgtagagctcatccatgc 28 18 29 DNA Artificial Sequence PCR Primer 18 attggtagctgtttcctgtg tgaaattgt 29 19 29 DNA Artificial Sequence PCR Primer 19ttaggttaag ccagccccga cacccgcca 29 20 25 DNA Artificial Sequence PCRPrimer 20 ggcatggcta gcaaaggaga agaac 25 21 28 DNA Artificial SequencePCR Primer 21 cggttatttg tagagctcat ccatgcca 28 22 29 DNA ArtificialSequence PCR Primer 22 gccttagctg tttcctgtgt gaaattgtt 29 23 29 DNAArtificial Sequence PCR Primer 23 ccgttttaag ccagccccga cacccgcca 29 2425 DNA Artificial Sequence PCR Primer 24 aaaatggcta gcaaaggaga agaac 2525 29 DNA Artificial Sequence PCR Primer 25 ttaggttatt tgtagagctcatccatgcc 29 26 29 DNA Artificial Sequence PCR Primer 26 attttcgagctgtttcctgt gtgaaattg 29 27 29 DNA Artificial Sequence PCR Primer 27taaccttaag ccagccccga cacccgcca 29 28 24 DNA Artificial Sequence PCRPrimer 28 ccatggctag caaaggagaa gaac 24 29 29 DNA Artificial SequencePCR Primer 29 gccttatttg tagagctcat ccatgccat 29 30 28 DNA ArtificialSequence PCR Primer 30 ggttagctgt ttcctgtgtg aaattgtt 28 31 29 DNAArtificial Sequence PCR Primer 31 ggcttttaag ccagccccga cacccgcca 29 3221 DNA Artificial Sequence PCR Primer 32 cggctggtcg acgcgggttt a 21 3315 DNA Artificial Sequence PCR Primer 33 aactcaatgg tgatg 15 34 41 DNAArtificial Sequence PCR Primer 34 aaaaaagctc ttctcatcct gacaagaacacgaactgaga t 41 35 44 DNA Artificial Sequence PCR Primer 35 ttttttgctcttcaaaaccc caagacaatt ctgcagatat ccag 44 36 48 DNA Artificial SequencePCR Primer 36 ttttttgcta gcgcggagcc gttttttgct cttcaaaacc ccaagaca 48 3720 DNA Artificial Sequence PCR Product 37 tgtttagccg gtttggtcgt 20 38 21DNA Artificial Sequence PCR Primer 38 ttgatccgtt gatcacggcg t 21 39 21DNA Artificial Sequence PCR Primer 39 cactatgcgt tatcgtacgc a 21 40 140DNA Artificial Sequence Experimental PCR Product 40 tcgttttaaatagatcttac agtatcacta ctccatctca gttcgtgttc ttgtcaggat 60 gagaagagcttttttgctag cgcggagccg ttttttgctc ttcaaaaccc caagacaatt 120 ctgcagatatccagcacagt 140 41 140 DNA Artificial Sequence Experimental PCR Product41 agcaaaattt atctagaatg tcatagtgat gaggtagagt caagcacaag aacagtccta 60ctcttctcga aaaaacgatc gcgcctcggc aaaaaacgag aagttttggg gttctgttaa 120gacgtctata ggtcgtgtca 140 42 29 DNA Artificial Sequence PCR Primer 42ggcttagctg tttcctgtgt gaaattgtt 29 43 25 DNA Artificial Sequence PCRPrimer 43 gccatggcta gcaaaggaga agaac 25 44 238 DNA Artificial SequenceExperimental PCR Product 44 gactcttcaa gcgcaagagc gcccaatacg caaaccgcctctccccgcgc gttggccgat 60 tcattaatgc agctggcacg acaggtttcc cgactggaaagcgggcagtg agcgcaacgc 120 aattaatgtg agttagctca ctcattaggc accccaggctttacacttta tgcttccggc 180 tcgtatgttg tgtggaattg tgagcggata acaatttcacacaggaaaca gctaagcc 238 45 723 DNA Artificial Sequence Experimental PCRProduct 45 gccatgagta aaggagaaga acttttcact ggagttgtcc caattcttgttgaattagat 60 ggtgatgtta atgggcacaa attttctgtc agtggagagg gtgaaggtgatgcaacatac 120 ggaaaactta cccttaaatt tatttgcact actggaaaac tacctgttccatggccaaca 180 cttgtcacta ctttctctta tggtgttcaa tgcttttcaa gatacccagatcatatgaaa 240 cggcatgact ttttcaagag tgccatgccc gaaggttatg tacaggaaagaactatattt 300 ttcaaagatg acgggaacta caagacacgt gctgaagtca agtttgaaggtgataccctt 360 gttaatagaa tcgagttaaa aggtattgat tttaaagaag atggaaacattcttggacac 420 aaattggaat acaactataa ctcacacaat gtatacatca tggcagacaaacaaaagaat 480 ggaatcaaag ttaacttcaa aattagacac aacattgaag atggaagcgttcaactagca 540 gaccattatc aacaaaatac tccaattggc gatggccctg tccttttaccagacaaccat 600 tacctgtcca cacaatctgc cctttcgaaa gatcccaacg aaaagagagaccacatggtc 660 cttcttgagt ttgtaacagc tgctgggatt acacatggca tggatgaactatacaaatga 720 ccg 723 46 30 DNA Artificial Sequence PCR Primer 46atgcccgcta gcaaaggaga agaacttttc 30 47 30 DNA Artificial Sequence PCRProduct 47 tttccctttg tagagctcat ccatgccatg 30 48 25 DNA ArtificialSequence PCR Primer 48 cttacgtact tgcaccatcc atgga 25 49 25 DNAArtificial Sequence PCR Primer 49 cttacgtact tgcaccatcc atgga 25 50 25DNA Artificial Sequence PCR Primer 50 aggtacctac cacgttcatg cattc 25 5142 DNA Artificial Sequence PCR Primer 51 cttacgtact tgcaccatccatggatggtg caagtacgta ag 42 52 42 DNA Artificial Sequence PCR Primer 52gaatgcatga acgtggtagg tacctaccac gttcatgcat tc 42

What is claimed is:
 1. A method of joining double strandedpolynucleotides which comprises: a. generating 5′ complementary cohesiveends on two or more polynucleotides by treating the polynucleotides witha DNA polymerase having 3′ to 5′ exonuclease activity and 5′ to 3′polymerizing activity in the presence of less than all of the dNTPsselected from the group consisting of dGTP, dCTP, dATP and dTTP whereincomplementary 5′ overhangs are produced; b. allowing the complementarycohesive ends to anneal wherein at least one of the polynucleotides hasa 5′ phosphate group using a DNA kinase treatment if necessary; and c.ligating the annealed complementary cohesive ends by treating of a DNAligase; wherein the DNA kinase treatment, DNA polymerase treatment, andDNA ligase treatment are performed in any one of the followingcombinations: DNA kinase followed by DNA polymerase, followed by DNAligase; DNA kinase and DNA polymerase co-treatment followed by DNAligase treatment; DNA polymerase, followed by DNA kinase, followed byligase; DNA polymerase followed by DNA kinase and DNA ligaseco-treatment; DNA kinase followed by DNA polymerase and DNA ligaseco-treatment; and wherein the DNA kinase treatment may be optional. 2.The method of claim 1, wherein the kinase reaction of at least one ofthe DNA fragments is stopped prior to being combined with other DNAfragments.
 3. The method of claim 1 wherein the 5′ phosphate group isadded to the polynucleotide in the presence of the DNA polymerase byadding a polynucleotide kinase to the reaction mixture in step (a). 4.The method of claim 3 wherein the DNA polymerase, DNA ligase andpolynucleotide kinase reactions are accomplished concurrently.
 5. Themethod of claim 4 wherein the DNA polymerase and polynucleotide kinasereactions occur before the DNA ligase reaction.
 6. The method of claim 4where the final recombinant molecule(s) will be amplified by PCR.
 7. Themethod of claim 4 where the final recombinant molecule(s) or PCRproducts thereof are used for in vitro transcription and/or in vitrotranscription/translation reactions.
 8. The method of claim 4 where thefinal recombinant molecule(s) or PCR products thereof are used for invivo transcription and/or in vivo transcription/translation reactions.9. A method for construction of recombinant DNA molecules as set forthclaim 1, or 4, wherein the recombinant DNA is constructed with the useof automated liquid handlers.
 10. A method for construction ofrecombinant DNA molecules through the method of claim 1, or 4 whereinthe resulting recombinant DNA is to be replicated in a living cell. 11.A method for construction of recombinant DNA molecules as set forth inclaim 1, or 4 where the recombinant DNA is to be used for constructingds RNAs for applications in RNAi.
 12. A method for construction ofrecombinant DNA molecules as set forth in claim 1, or 4 where therecombinant DNA is to be used for constructing ds hairpin RNAs forapplications in RNAi.
 13. A method for construction of recombinant DNAmolecules as set forth in claim 1, or 4 where the recombinant DNA is tobe used in in vitro transcription reactions.
 14. A method forconstruction of recombinant DNA molecules as set forth in claim 1, or 4where the recombinant DNA is to be used in in vitro transcriptionreactions.
 15. A method for construction of recombinant DNA molecules asset forth in claim 1, or 4 where the recombinant DNA is to be used in invitro transcription/translation reactions.
 16. A method for constructionof recombinant DNA molecules as set forth in claim 1, or 4 where therecombinant DNA is to be used in in vivo transcription/translation/geneexpression studies.
 17. A composition of DNA polymerase, in the presenceof a subset of all 4 dNTPs, DNA kinase and DNA ligase activities whichfunction to efficiently generate recombinant DNAs by either maintainingcomplementary 5′ single stranded overhangs between multiple DNAs,kinasing the 5′ ends of DNAs, if necessary and allowing DNAs to annealthrough the complementary overhangs and be covalently joined by the DNAligase activity.
 18. A composition of DNA polymerase, in the presence ofa subset of all 4 dNTPs, DNA kinase and DNA ligase activities whichfunction to efficiently generate recombinant DNAs by either generatingcomplementary 5′ single stranded overhangs between multiple DNAs,kinasing the 5′ ends of DNAs, if necessary and allowing DNAs to annealthrough the complementary overhangs and be covalently joined by the DNAligase activity.
 19. A composition of DNA polymerase, in the presence ofa subset of all 4 dNTPs, and DNA kinase which functions to efficientlygenerate 5′ single stranded overhangs on at least one end of a ds DNAmolecule, and efficiently adds a phosphate group to 5′ ends of DNA, ifnecessary.
 20. A composition of DNA polymerase, in the presence of asubset of all 4 dNTPs, and DNA kinase which functions to efficientlymaintain 5′ single stranded overhangs on at least one end of a ds DNAmolecule, and efficiently adds a phosphate group to 5′ ends of DNA, ifnecessary.
 21. A composition of DNA polymerase, in the presence of asubset of all 4 dNTPs, and DNA ligase which functions to efficientlygenerate 5′ single stranded overhangs on at least one end of a ds DNAmolecule, and allows DNAs with complementary 5′ single strandedoverhangs to anneal and be efficiently joined by DNA ligase.
 22. Acomposition of DNA polymerase, in the presence of a subset of all 4dNTPs, and DNA ligase which functions to efficiently maintain 5′ singlestranded overhangs on at least one end of a ds DNA molecule, and allowsDNAs with complementary 5′ single stranded overhangs to anneal and beefficiently joined by DNA ligase.
 23. A computer controlled method foreffecting any one of the plurality of processes as shown in FIGS. 15-17for construction of recombinant DNA.
 24. An apparatus for computercontrolling any one of the plurality of processes as shown in FIGS.15-17 for construction of recombinant DNA.